chebuu
The first infectious cause of cancer was identified in 1911 by Peyton Rous who demonstrated the transmissibility of a tumor in fowl through injection of sub 0.2 micron filtrate of the tumor .
## Skipping install of 'HPVSerovars' from a github remote, the SHA1 (17418f04) has not changed since last install.
## Use `force = TRUE` to force installation
(Not run) This vignette is packaged and accessible via: browseVignettes('HPVSerovars').
Download OligoArrayAux and see the following vignette for installation instructions.
library(devtools)
devtools::install_github('chebuu/Design-Group-Specific-Primers')
library(Design_Group_Specific_Primers)
vignette('Installing-OligoArrayAux', package = 'Design_Group_Specific_Primers')From the openPimer vignette:
openPrimeR requires external programs for some features, particularly for computing the physicochemical properties of primers. Please make sure you have the following tools installed on your system such that they are in your system’s path:
MELTING (>= 5.1.1): For melting temperature computations. ViennaRNA (>= 2.2.4): For secondary structure prediction. OligoArrayAux (>= 3.8): For primer efficiency computations as performed by DECIPHER. MAFFT (>= 7.305): For computing multiple sequence alignments. Pandoc (>= 1.19.1): For creating PDF reports.
If you would like to be able to access the immunoglobulin repository IMGT from the openPrimeR Shiny app, you should additionally fulfill the following dependencies:
PhantomJS (>= 2.1): For headless website calls. Python (>=2.7.9) and the selenium (>=3.0.1) module: For data extraction scripts. openPrimeR will automatically check for all dependencies and inform you about any missing dependencies when the package is attached:
Note that the tool is still functional if there are missing external programs. However, we recommend that all dependencies are fulfilled to guarantee the best user experience.
# Install from Bioconductor
if (!requireNamespace("BiocManager", quietly = T))
install.packages("BiocManager")
BiocManager::install("Biostrings")
BiocManager::install("DECIPHER")
# Open Biostrings vignettes
library(Biostrings)
browseVignettes("Biostrings")
# Open DECIPHER docs and vignettes
library(DECIPHER)
help("DECIPHER")
browseVignettes("DECIPHER")doAlignment <- function(xset) {
useqs <- unique(xset)
uidxs <- match(xset, useqs)
aseqs <- AlignSeqs(useqs, verbose=F)
aseqs[uidxs]
}Some references to remind me of packages, methods, etc.:
# CRAN
# https://rdrr.io/cran/dpcR/f/vignettes/overview.Rmd
# BIOC
# https://bioconductor.org/packages/release/bioc/html/twoddpcr.html
# https://bioconductor.org/packages/release/bioc/html/ddCt.html
# https://bioconductor.org/packages/3.5/bioc/html/mBPCR.html
# Other
# https://doi.org/10.1007/s13402-017-0331-y
I copied the tables from Wiki: Human_papillomavirus_infection and included them in the R package assoc. w/ this document github.com/Chebuu/HPV-Serovars.
The Wiki data contains phenotypic categorizations of several HPV strains. It’s useful for testing.
HPV <- c(HPV.Sequelae, HPV.GenitalCancerRisk)
p.1 <- unique(unlist(HPV))
knitr::kable(
sprintf('HPV-%s', sort(p.1)), col.names = '',
caption = sprintf(
'Unique HPV serotypes (N=%s) (Total=%s): ',
length(p.1), length(HPV)
)
)| HPV-1 |
| HPV-2 |
| HPV-3 |
| HPV-4 |
| HPV-6 |
| HPV-7 |
| HPV-10 |
| HPV-11 |
| HPV-13 |
| HPV-16 |
| HPV-18 |
| HPV-22 |
| HPV-26 |
| HPV-28 |
| HPV-31 |
| HPV-32 |
| HPV-33 |
| HPV-35 |
| HPV-39 |
| HPV-42 |
| HPV-44 |
| HPV-45 |
| HPV-51 |
| HPV-52 |
| HPV-53 |
| HPV-56 |
| HPV-58 |
| HPV-59 |
| HPV-60 |
| HPV-63 |
| HPV-66 |
| HPV-68 |
| HPV-73 |
| HPV-82 |
Unique HPV serotypes (N=34) (Total=13):
## $`Common warts`
## [1] 2 7 22
##
## $`Plantar warts`
## [1] 1 2 4 63
##
## $`Flat warts`
## [1] 3 10 28
##
## $`Anogenital warts`
## [1] 6 11 42 44
Reference genomes for all serovars listed in data(HPV.Sequelae)and data(HPV.GenitalCancerRisk)were selected from among the results of the following PaVEPaVE query:
https://pave.niaid.nih.gov/#search/search_database/kw
?dbNamespace=Genomes
&includeNR=true
&refCloneOnly=false
&sort=Locus_ID
&sortType=true
&page=600&start=1
&text=Human&showTable=1
&
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
## Loading required package: BiocGenerics
## Loading required package: parallel
##
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
##
## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
## clusterExport, clusterMap, parApply, parCapply, parLapply,
## parLapplyLB, parRapply, parSapply, parSapplyLB
## The following objects are masked from 'package:dplyr':
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##
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##
## anyDuplicated, append, as.data.frame, basename, cbind, colnames,
## dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
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## order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
## rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
## union, unique, unsplit, which, which.max, which.min
## Loading required package: S4Vectors
## Warning: package 'S4Vectors' was built under R version 3.6.3
## Loading required package: stats4
##
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## collapse, desc, slice
## Loading required package: XVector
##
## Attaching package: 'Biostrings'
## The following object is masked from 'package:base':
##
## strsplit
## Loading required package: RSQLite
# data(PaVE.Wikiv)
data(HPV.REF.PaVE.seqs)
data(HPV.REF.PaVE.vars)
testVars <- lapply(grep('[1-9]*', HPV.REF.PaVE.vars, value = T), function(x) {
sapply(HPV.Sequelae, function(y) any(x %in% y))
})
dbConn <- dbConnect(SQLite(), ':memory:')
DECIPHER::Seqs2DB(HPV.REF.PaVE.seqs, 'XStringSet', dbConn, '')## Adding 218 sequences to the database.
##
## 218 total sequences in table Seqs.
## Time difference of 0.31 secs
DECIPHER::Add2DB(
data.frame(
# identifier = testVars
identifier = lapply(HPV.REF.PaVE.vars, function(x) grep('[1-9]', x, perl = T))
),
dbConn, verbose = F
)
# # DEL
# library(Biostrings)
# PaVE.Wikiv<-Biostrings::readDNAStringSet('../inst/extdata/HPV.REFS.PaVE.wikivars.fasta')
# usethis::use_data(PaVE.Wikiv)
#
# https://www.youtube.com/watch?v=zu8Z9-kebKQ&list=PLjiXAZO27elDHGlQwfd06r7coiFtpPkvI&index=5
#
# # ENDlibrary(dplyr)
library(tidyr)
library(stringr)
library(Biostrings)
library(DECIPHER)
library(HPVSerovars)I included GenBank queries for all the HPV DNA in this repo. If you want to run them just paste in the search bar at: https://www.ncbi.nlm.nih.gov/nuccore
https://www.ncbi.nlm.nih.gov/nuccore
"Human papillomavirus"[Primary Organism]
AND viruses[filter]
NOT Polyamides[All Fields]
NOT Method[All Fields]
NOT Patent[All Fields]https://www.ncbi.nlm.nih.gov/nuccore
https://www.ncbi.nlm.nih.gov/nuccore
"Human papillomavirus"[Primary Organism]
AND viruses[filter]
NOT Polyamides[All Fields]
NOT Method[All Fields]
NOT Patent[All Fields]
AND Oral[All Fields] A collection of l1 DNA sequences (avg. ~600bp) from various oral isolates of HPV (extracted from results of GenBank query above) are aligned and loaded in SQLite (RAM) along with annotations from GenBank that describe the serotype of each isolate.
# library(HPVSerovars)
#
# data(Oral.L1.seqs)
# data(Oral.L1.vars)
load('../data/Oral.L1.seqs.rda')
load('../data/Oral.L1.vars.rda')
dbConn <- dbConnect(SQLite(), ':memory:')
# Oral.L1.seqs <- readDNAStringSet('../inst/extdata/HPV.oral.L1.fasta') %>% doAlignment
# Oral.L1.vars <- read.csv('../inst/extdata/HPV.oral.L1.csv', stringsAsFactors = F)
Seqs2DB(Oral.L1.seqs, 'XStringSet', dbConn, '')## Adding 31 sequences to the database.
##
## 31 total sequences in table Seqs.
## Time difference of 0.02 secs
## Expression:
## alter table Seqs add column GI INTEGER
##
## Expression:
## update Seqs set GI = :GI where row_names = :row_names
##
## Expression:
## alter table Seqs add column SVAR INTEGER
##
## Expression:
## update Seqs set SVAR = :SVAR where row_names = :row_names
## Warning: Factors converted to character
## Expression:
## alter table Seqs add column ISO INTEGER
##
## Expression:
## update Seqs set ISO = :ISO where row_names = :row_names
##
## Expression:
## alter table Seqs add column GENE INTEGER
##
## Expression:
## update Seqs set GENE = :GENE where row_names = :row_names
## Warning: Factors converted to character
## Expression:
## update Seqs set identifier = :identifier where row_names = :row_names
## Warning: Factors converted to character
## Added to table Seqs: "GI" and "SVAR" and "ISO" and "GENE" and "identifier".
##
## Time difference of 0.04 secs
## row_names identifier
## 1 1 HPV18
## 2 2 HPV18
## 3 3 HPV16
## 4 4 HPV18
## description
## 1 gi|944543704|gb|KT365847.1| Human papillomavirus isolate HPV18-14 L1 protein gene, partial cds
## 2 gi|944543703|gb|KT365846.1| Human papillomavirus isolate HPV18-13 L1 protein gene, partial cds
## 3 gi|944543701|gb|KT365845.1| Human papillomavirus isolate HPV16-5 L1 protein gene, partial cds
## 4 gi|944543699|gb|KT365844.1| Human papillomavirus isolate HPV18-12 L1 protein gene, partial cds
## GI SVAR ISO GENE
## 1 944543704 HPV18 14 L1
## 2 944543703 HPV18 13 L1
## 3 944543701 HPV16 5 L1
## 4 944543699 HPV18 12 L1
Design HPV16-specific F/R primers using DECIPHER utilities.
## Warning in TileSeqs(dbFile = dbConn, minLength = 18, maxLength = 29, minCoverage
## = 0.8): Skipped due to multiple width sequences: HPV18
## Warning in TileSeqs(dbFile = dbConn, minLength = 18, maxLength = 29, minCoverage
## = 0.8): Skipped due to multiple width sequences: HPV16
## ================================================================
## Warning in TileSeqs(dbFile = dbConn, minLength = 18, maxLength = 29, minCoverage
## = 0.8): Skipped due to multiple width sequences: HPV17
##
##
## Time difference of 2.92 secs
## misprime target_site
## 1 FALSE TCCTAAGCAGGGTGACAATGTGGATAGCA
## 2 FALSE CTAAGCAGGTACAAATGCTTATTGTGGGC
## 3 FALSE AGATTAGTTTGGCGACTGGTAGGACTTCA
## 4 FALSE GCCAGCAGTTCTAGACTCCTTGCTGTGGG
## 5 FALSE GGGCATCCATTGCTAAACAAATATGATGA
## 6 FALSE GCAGTTCTAGACTCCTTGCTGTGGGACAT
oligos.L1 <- DesignPrimers(
tiles = tiles.L1,
identifier = 'HPV4',
worstScore = -1E3,
maxPermutations = 5,
minGroupCoverage = 0.85,
minCoverage = 0.85,
minLength = 20,
maxLength = 28
)##
## HPV4 (324 candidate primers):
## ================================================================================
##
## Time difference of 7.1 secs
## identifier start_forward start_reverse start_aligned_forward
## 3 HPV4 37 52 30
## 4 HPV4 37 53 31
## 5 HPV4 38 54 32
## 6 HPV4 38 55 33
## 7 HPV4 39 55 34
## 8 HPV4 40 55 35
## start_aligned_reverse permutations_forward permutations_reverse score_forward
## 3 58 1 1 0
## 4 59 1 1 0
## 5 60 1 1 0
## 6 61 1 1 0
## 7 62 1 1 0
## 8 63 1 1 0
## score_reverse forward_primer.1 forward_primer.2 forward_primer.3
## 3 0 TGGTCCCAAAGGTTTCAGCAAA <NA> <NA>
## 4 0 TGGTCCCAAAGGTTTCAGCAAAT <NA> <NA>
## 5 0 GGTCCCAAAGGTTTCAGCAAATC <NA> <NA>
## 6 0 GGTCCCAAAGGTTTCAGCAAATCA <NA> <NA>
## 7 0 GTCCCAAAGGTTTCAGCAAATCAG <NA> <NA>
## 8 0 TCCCAAAGGTTTCAGCAAATCAGT <NA> <NA>
## forward_primer.4 forward_primer.5 reverse_primer.1 reverse_primer.2
## 3 <NA> <NA> GAAACCTTTGGGACCACAATTTT <NA>
## 4 <NA> <NA> TGAAACCTTTGGGACCACAATTT <NA>
## 5 <NA> <NA> CTGAAACCTTTGGGACCACAATT <NA>
## 6 <NA> <NA> GCTGAAACCTTTGGGACCACAAT <NA>
## 7 <NA> <NA> GCTGAAACCTTTGGGACCACAA <NA>
## 8 <NA> <NA> GCTGAAACCTTTGGGACCACA <NA>
## reverse_primer.3 reverse_primer.4 reverse_primer.5 forward_efficiency.1
## 3 <NA> <NA> <NA> 0.8695543
## 4 <NA> <NA> <NA> 0.8997148
## 5 <NA> <NA> <NA> 0.9171716
## 6 <NA> <NA> <NA> 0.9356067
## 7 <NA> <NA> <NA> 0.8303409
## 8 <NA> <NA> <NA> 0.9161453
## forward_efficiency.2 forward_efficiency.3 forward_efficiency.4
## 3 NA NA NA
## 4 NA NA NA
## 5 NA NA NA
## 6 NA NA NA
## 7 NA NA NA
## 8 NA NA NA
## forward_efficiency.5 reverse_efficiency.1 reverse_efficiency.2
## 3 NA 0.8433773 NA
## 4 NA 0.8369640 NA
## 5 NA 0.8697235 NA
## 6 NA 0.9333216 NA
## 7 NA 0.9122828 NA
## 8 NA 0.8831295 NA
## reverse_efficiency.3 reverse_efficiency.4 reverse_efficiency.5
## 3 NA NA NA
## 4 NA NA NA
## 5 NA NA NA
## 6 NA NA NA
## 7 NA NA NA
## 8 NA NA NA
## forward_coverage.1 forward_coverage.2 forward_coverage.3 forward_coverage.4
## 3 1 NA NA NA
## 4 1 NA NA NA
## 5 1 NA NA NA
## 6 1 NA NA NA
## 7 1 NA NA NA
## 8 1 NA NA NA
## forward_coverage.5 reverse_coverage.1 reverse_coverage.2 reverse_coverage.3
## 3 NA 1 NA NA
## 4 NA 1 NA NA
## 5 NA 1 NA NA
## 6 NA 1 NA NA
## 7 NA 1 NA NA
## 8 NA 1 NA NA
## reverse_coverage.4 reverse_coverage.5 mismatches_forward mismatches_reverse
## 3 NA NA
## 4 NA NA
## 5 NA NA
## 6 NA NA
## 7 NA NA
## 8 NA NA
Honestly, I don’t really understand the dimensions of the dataframe output by DECIPHER::DesignPimers. If I remember correctly, it’s a 7x17 matrix where each cell holds a list of 5 oligos. Unfortunately, I can’t print the matrix to stdout, which makes debugging slow, so I’ll just deal with this issue later I guess…
Plot hybridization curves for the reverse compliment of each primer pair (5) in each primer set (7).
plotMeltCurves <- function(temps, effs) {
plot(
temps, effs[,1], ylim=c(0,1),
ylab="Hybridization Efficiency",
xlab=expression(paste("Temperature (", degree, "C)", sep="")),
type="l", lwd=2, col="Blue", main="Denaturation Plot"
)
lines(temps, effs[,2], col="Red", lwd=2)
abline(h=0.5, lty=2, lwd=2, col="Orange")
abline(v=64, lty=2, lwd=2, col="Green")
legend(
"topright",
legend = c(
"Forward Primer",
"Reverse Primer",
"50% Efficiency",
"Annealing Temperature"
),
col = c("Blue", "Red", "Orange", "Green"),
lwd = c(2, 2, 2, 2), lty = c(1, 1, 2, 2)
)
}
meltCurves <-
function(primers, target=reverseComplement(DNAStringSet(primers)), temps=60:75, P=4e-7, ions=.225, doPlot=TRUE, ...) {
fxn <- function(temp) CalculateEfficiencyPCR(primers, target, temp, P=P, ions=ions, ...)
effs <- matrix(unlist(lapply(temps, fxn)), ncol=2, byrow=TRUE)
if (doPlot) plotMeltCurves(temps, effs)
list(temps = temps, effs = effs)
}
nsets <- nrow(oligos.L1)
npair <- ncol(oligos.L1)
for (i in 1:nsets)
for (j in 1:npair)
tryCatch(
{
c(
oligos.L1$forward_primer[i,j],
oligos.L1$reverse_primer[i,j]
) %>% meltCurves
},
error = function(e) NULL
# # ¿ --- It's supposed to be 7o x 17p --- ?
# warning(sprintf('%s [iteration i=%s j=%s]', e, i, j))
)More primer designs (RFLP, sequencing, etc.):
TYPE <- 'sequence'
MIN_LENGTH <- 15
MAX_LENGTH <- 25
MIN_SIZE <- 60
MAX_SIZE <- 100
LEVELS <- 2
RESOLUTION <- 3
ENZYMES <- NULL
DesignSignatures(
dbConn,
type = TYPE,
minLength = MIN_LENGTH,
maxLength = MAX_LENGTH,
minProductSize = MIN_SIZE,
maxProductSize = MAX_SIZE,
resolution = RESOLUTION,
levels = LEVELS,
enzymes = ENZYMES
)## Tallying 8-mers for 5 groups:
## ================================================================================
##
## Time difference of 0.48 secs
##
## Designing primer sequences based on the group 'HPV18':
## ================================================================================
##
## Time difference of 67.94 secs
##
## Selecting the most common primer sequences:
## ================================================================================
##
## Time difference of 14.97 secs
##
## Determining PCR products from each group:
## ================================================================================
##
## Time difference of 3.04 secs
##
## Scoring primer pair combinations:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Choosing optimal forward and reverse pairs:
## ================================================================================
##
## Time difference of 1.71 secs
## forward_primer reverse_primer score coverage products
## 1 CCAACGACGCAGAGAAACACAA ATGTCTTGCAATGTTGCCTTAGGT 0 0.2 0
## 2 CCAACGACGCAGAGAAACACAAG ATGTCTTGCAATGTTGCCTTAGGT 0 0.2 0
## 3 GCTTTGAGGATCCAACACGGC GCAGTGAAGTGTTCAGTTCCGT 0 0.2 0
## 4 GCTTTGAGGATCCAACACGGC GTGTTCAGTTCCGTGCACAGAT 0 0.2 0
## 5 GCTTTGAGGATCCAACACGGC GCAGTGAAGTGTTCAGTTCCGTG 0 0.2 0
## 6 GCTTTGAGGATCCAACACGGC AGTGTTCAGTTCCGTGCACAG 0 0.2 0
## 7 GCTTTGAGGATCCAACACGGC AGTGAAGTGTTCAGTTCCGTGC 0 0.2 0
## 8 GCTTTGAGGATCCAACACGGC GTGTTCAGTTCCGTGCACAGA 0 0.2 0
## 9 GCTTTGAGGATCCAACACGGC GTGAAGTGTTCAGTTCCGTGCA 0 0.2 0
## 10 GCTTTGAGGATCCAACACGGC GAAGTGTTCAGTTCCGTGCACA 0 0.2 0
## 11 TCGTGCTGCAACCGAGC ATGTCTTGCAATGTTGCCTTAGGT 0 0.2 0
## 12 TCGTGCTGCAACCGAGC GTTGCCTTAGGTCCATGCATACTTA 0 0.2 0
## 13 CAGGAAMGACTCCAACGACGC ATGTCTTGCAATGTTGCCTTAGGT 0 0.2 0
## 14 CAGGAAMGACTCCAACGACGC GTTGCCTTAGGTCCATGCATACTTA 0 0.2 0
## 15 GGAAMGACTCCAACGACGC ATGTCTTGCAATGTTGCCTTAGGT 0 0.2 0
## 16 GGAAMGACTCCAACGACGC GTTGCCTTAGGTCCATGCATACTTA 0 0.2 0
## 17 CCCCCCCGCCAACTACTA GTGCAGCATCCTTTTGACAGGT 0 0.2 0
## 18 CCCCCCCGCCAACTACTA CCTTATTTTCAGCYGGTGCAGCAT 0 0.2 0
## 19 CCCCCCCGCCAACTACTA TTTCAGCYGGTGCAGCAT 0 0.2 0
## 20 CCCCCCCGCCAACTACTA GTGCAGCATCCTTTTGACAGGTAAT 0 0.2 0
## 21 CCCCCCCGCCAACTACTA CCTTATTTTCAGCYGGTGCAGCATC 0 0.2 0
## 22 CCCCCCCGCCAACTACTA TCCTTATTTTCAGCYGGTGCAGC 0 0.2 0
## 23 CCCCCCCGCCAACTACTA CCTTATTTTCAGCYGGTGCAGC 0 0.2 0
## 24 CCCCCCCGCCAACTACTA GTGCAGCATCCTTTTGACAGGTA 0 0.2 0
## 25 CCCCCCCGCCAACTACTA CCTTATTTTCAGCYGGTGCAGCA 0 0.2 0
## 26 CCCCCCCGCCAACTACTA TTTCAGCYGGTGCAGCA 0 0.2 0
## 27 CCCCCCCGCCAACTACTA GTGCAGCATCCTTTTGACAGGTAA 0 0.2 0
## 28 TCTCCTGTACCTGGGCAATATGAT TCYTCAACATGTCTGCTATACTGCT 0 0.2 0
## 29 TCTCCTGTACCTGGGCAATATGAT CCTCAACATGTCTGCTATACTGCC 0 0.2 0
## 30 GCATGCTGCATGCCATAAATGTATA TCYAATGTGTCTCCATACACAGAGT 0 0.2 0
## 31 TGCCGCCACGTCTAATGTTTC GGCACAGCCCAAAATACATAACTGT 0 0.2 0
## 32 TGCCGCCACGTCTAATGTTTC GGGCACAGCCCAAAATACATAACT 0 0.2 0
## 33 TGCCGCCACGTCTAATGTTTC GGGCACAGCCCAAAATACATAACTG 0 0.2 0
## 34 TGCCGCCACGTCTAATGTTTC CAATAGCAGGGGCACAGCC 0 0.2 0
## 35 TGCCGCCACGTCTAATGTTTC GGGGCACAGCCCAAAATACATAAC 0 0.2 0
## 36 TGCCGCCACGTCTAATGTTTC GCAGGGKYACAGCCCA 0 0.2 0
## 37 CAACGACGCAGAGAAACACAAGTAT ATGTCTTGCAATGTTGCCTTAGGT 0 0.2 0
## 38 GATGTGAGAAACRCACCACAATACT GCTTGTAGGGTCGCCGTGTT 0 0.2 0
## 39 GATGTGAGAAACRCACCACAATACT GCTTGTAGGGTCGCCGTGT 0 0.2 0
## 40 GATGTGAGAAACRCACCACAATACT CACAGATCAGGTAGCTTGTAGGGT 0 0.2 0
## 41 GATGTGAGAAACRCACCACAATACT AGTTCCGTGCACAGATCAGGT 0 0.2 0
## 42 GATGTGAGAAACRCACCACAATACT GTGTTCAGTTCCGTGCACAGAT 0 0.2 0
## 43 GATGTGAGAAACRCACCACAATACT CTTGTAGGGTCGCCGTGTTG 0 0.2 0
## 44 GATGTGAGAAACRCACCACAATACT GCTTGTAGGGTCGCCGTG 0 0.2 0
## 45 GATGTGAGAAACRCACCACAATACT GTAGGGTCGCCGTGTTGG 0 0.2 0
## 46 GATGTGAGAAACRCACCACAATACT GCACAGATCAGGTAGCTTGTAGGG 0 0.2 0
## 47 GATGTGAGAAACRCACCACAATACT CAGTTCCGTGCACAGATCAGG 0 0.2 0
## 48 GATGTGAGAAACRCACCACAATACT AGATCAGGTAGCTTGTAGGGTCG 0 0.2 0
## 49 GATGTGAGAAACRCACCACAATACT GTAGCTTGTAGGGTCGCCG 0 0.2 0
## 50 GATGTGAGAAACRCACCACAATACT GTTCCGTGCACAGATCAGGTAG 0 0.2 0
## 51 GATGTGAGAAACRCACCACAATACT GTTCAGTTCCGTGCACAGATCAG 0 0.2 0
## 52 GATGTGAGAAACRCACCACAATACT ACAGATCAGGTAGCTTGTAGGGTC 0 0.2 0
## 53 GATGTGAGAAACRCACCACAATACT TGTTCAGTTCCGTGCACAGATC 0 0.2 0
## 54 GATGTGAGAAACRCACCACAATACT TCAGGTAGCTTGTAGGGTCGC 0 0.2 0
## 55 GATGTGAGAAACRCACCACAATACT AGGTAGCTTGTAGGGTCGCC 0 0.2 0
## 56 GATGTGAGAAACRCACCACAATACT AGTTCCGTGCACAGATCAGGTA 0 0.2 0
## 57 GATGTGAGAAACRCACCACAATACT GTGTTCAGTTCCGTGCACAGA 0 0.2 0
## 58 GATGTGAGAAACRCACCACAATACT GTTCAGTTCCGTGCACAGATCA 0 0.2 0
## 59 TCTGAGGACGTTAGGGACAATGTG GGCACAGCCCAAAATACATAACTGT 0 0.2 0
## 60 TCTGAGGACGTTAGGGACAATGTG GGGCACAGCCCAAAATACATAACT 0 0.2 0
## 61 TCTGAGGACGTTAGGGACAATGTG GGGCACAGCCCAAAATACATAACTG 0 0.2 0
## 62 TCTGAGGACGTTAGGGACAATGTG CAATAGCAGGGGCACAGCC 0 0.2 0
## 63 TCTGAGGACGTTAGGGACAATGTG GGGGCACAGCCCAAAATACATAAC 0 0.2 0
## 64 TCTGAGGACGTTAGGGACAATGTG GCAGGGKYACAGCCCA 0 0.2 0
## 65 CAACGACGCAGAGAAACACAAGT ATGTCTTGCAATGTTGCCTTAGGT 0 0.2 0
## 66 GCAGGTACTATGGGTGACACTGTG GCACGCATACCTGTGCCTTTAATAT 0 0.2 0
## 67 GCAGGTACTATGGGTGACACTGTG GCACGCATACCTGTGCCTTTAAT 0 0.2 0
## 68 GCAGGTACTATGGGTGACACTGTG GCACGCATACCTGTGCCTTTAA 0 0.2 0
## 69 CGGCTGGTTTTATGTACAGGCTA CCATATCCGACCCTGTGTCTGTT 0 0.2 0
## 70 CGGCTGGTTTTATGTACAGGCTA CCATATCCGACCCTGTGTCTGT 0 0.2 0
## 71 CGGCTGGTTTTATGTACAGGCTA ACCATATCCGACCCTGTGTCTG 0 0.2 0
## 72 CGGCTGGTTTTATGTACAGGCTA CGACCCTGTGTCTGTTGCATTTTC 0 0.2 0
## 73 ACTCTGTGTATGGAGACACATTGGA GCACCGCAGGCACCTTATTAAT 0 0.2 0
## 74 ACTCTGTGTATGGAGACACATTGGA GCACCGCAGGCACCTTATTAA 0 0.2 0
## 75 ACTCTGTGTATGGAGACACATTGGA GCACCGCAGGCACCTTATTAATAAA 0 0.2 0
## 76 AGATGTGAGAAACRCACCACAAT GCTTGTAGGGTCGCCGTGTT 0 0.2 0
## 77 AGATGTGAGAAACRCACCACAAT GCTTGTAGGGTCGCCGTGT 0 0.2 0
## 78 AGATGTGAGAAACRCACCACAAT CACAGATCAGGTAGCTTGTAGGGT 0 0.2 0
## 79 AGATGTGAGAAACRCACCACAAT AGTTCCGTGCACAGATCAGGT 0 0.2 0
## 80 AGATGTGAGAAACRCACCACAAT GTGTTCAGTTCCGTGCACAGAT 0 0.2 0
## 81 AGATGTGAGAAACRCACCACAAT CTTGTAGGGTCGCCGTGTTG 0 0.2 0
## 82 AGATGTGAGAAACRCACCACAAT GCTTGTAGGGTCGCCGTG 0 0.2 0
## 83 AGATGTGAGAAACRCACCACAAT GTAGGGTCGCCGTGTTGG 0 0.2 0
## 84 AGATGTGAGAAACRCACCACAAT GCACAGATCAGGTAGCTTGTAGGG 0 0.2 0
## 85 AGATGTGAGAAACRCACCACAAT CAGTTCCGTGCACAGATCAGG 0 0.2 0
## 86 AGATGTGAGAAACRCACCACAAT AGATCAGGTAGCTTGTAGGGTCG 0 0.2 0
## 87 AGATGTGAGAAACRCACCACAAT GTAGCTTGTAGGGTCGCCG 0 0.2 0
## 88 AGATGTGAGAAACRCACCACAAT GTTCCGTGCACAGATCAGGTAG 0 0.2 0
## 89 AGATGTGAGAAACRCACCACAAT GTTCAGTTCCGTGCACAGATCAG 0 0.2 0
## 90 AGATGTGAGAAACRCACCACAAT AGTGTTCAGTTCCGTGCACAG 0 0.2 0
## 91 AGATGTGAGAAACRCACCACAAT ACAGATCAGGTAGCTTGTAGGGTC 0 0.2 0
## 92 AGATGTGAGAAACRCACCACAAT TGTTCAGTTCCGTGCACAGATC 0 0.2 0
## 93 AGATGTGAGAAACRCACCACAAT AGTGAAGTGTTCAGTTCCGTGC 0 0.2 0
## 94 AGATGTGAGAAACRCACCACAAT TCAGGTAGCTTGTAGGGTCGC 0 0.2 0
## 95 AGATGTGAGAAACRCACCACAAT AGGTAGCTTGTAGGGTCGCC 0 0.2 0
## 96 AGATGTGAGAAACRCACCACAAT TGAAGTGTTCAGTTCCGTGCAC 0 0.2 0
## 97 AGATGTGAGAAACRCACCACAAT AGTTCCGTGCACAGATCAGGTA 0 0.2 0
## 98 AGATGTGAGAAACRCACCACAAT GTGTTCAGTTCCGTGCACAGA 0 0.2 0
## 99 AGATGTGAGAAACRCACCACAAT GTTCAGTTCCGTGCACAGATCA 0 0.2 0
## 100 AGATGTGAGAAACRCACCACAAT GTGAAGTGTTCAGTTCCGTGCA 0 0.2 0
## similar_signatures missing_signatures
## 1 HPV16, HPV11, HPV4, HPV17
## 2 HPV16, HPV11, HPV4, HPV17
## 3 HPV16, HPV11, HPV4, HPV17
## 4 HPV16, HPV11, HPV4, HPV17
## 5 HPV16, HPV11, HPV4, HPV17
## 6 HPV16, HPV11, HPV4, HPV17
## 7 HPV16, HPV11, HPV4, HPV17
## 8 HPV16, HPV11, HPV4, HPV17
## 9 HPV16, HPV11, HPV4, HPV17
## 10 HPV16, HPV11, HPV4, HPV17
## 11 HPV16, HPV11, HPV4, HPV17
## 12 HPV16, HPV11, HPV4, HPV17
## 13 HPV16, HPV11, HPV4, HPV17
## 14 HPV16, HPV11, HPV4, HPV17
## 15 HPV16, HPV11, HPV4, HPV17
## 16 HPV16, HPV11, HPV4, HPV17
## 17 HPV16, HPV11, HPV4, HPV17
## 18 HPV16, HPV11, HPV4, HPV17
## 19 HPV16, HPV11, HPV4, HPV17
## 20 HPV16, HPV11, HPV4, HPV17
## 21 HPV16, HPV11, HPV4, HPV17
## 22 HPV16, HPV11, HPV4, HPV17
## 23 HPV16, HPV11, HPV4, HPV17
## 24 HPV16, HPV11, HPV4, HPV17
## 25 HPV16, HPV11, HPV4, HPV17
## 26 HPV16, HPV11, HPV4, HPV17
## 27 HPV16, HPV11, HPV4, HPV17
## 28 HPV16, HPV11, HPV4, HPV17
## 29 HPV16, HPV11, HPV4, HPV17
## 30 HPV16, HPV11, HPV4, HPV17
## 31 HPV16, HPV11, HPV4, HPV17
## 32 HPV16, HPV11, HPV4, HPV17
## 33 HPV16, HPV11, HPV4, HPV17
## 34 HPV16, HPV11, HPV4, HPV17
## 35 HPV16, HPV11, HPV4, HPV17
## 36 HPV16, HPV11, HPV4, HPV17
## 37 HPV16, HPV11, HPV4, HPV17
## 38 HPV16, HPV11, HPV4, HPV17
## 39 HPV16, HPV11, HPV4, HPV17
## 40 HPV16, HPV11, HPV4, HPV17
## 41 HPV16, HPV11, HPV4, HPV17
## 42 HPV16, HPV11, HPV4, HPV17
## 43 HPV16, HPV11, HPV4, HPV17
## 44 HPV16, HPV11, HPV4, HPV17
## 45 HPV16, HPV11, HPV4, HPV17
## 46 HPV16, HPV11, HPV4, HPV17
## 47 HPV16, HPV11, HPV4, HPV17
## 48 HPV16, HPV11, HPV4, HPV17
## 49 HPV16, HPV11, HPV4, HPV17
## 50 HPV16, HPV11, HPV4, HPV17
## 51 HPV16, HPV11, HPV4, HPV17
## 52 HPV16, HPV11, HPV4, HPV17
## 53 HPV16, HPV11, HPV4, HPV17
## 54 HPV16, HPV11, HPV4, HPV17
## 55 HPV16, HPV11, HPV4, HPV17
## 56 HPV16, HPV11, HPV4, HPV17
## 57 HPV16, HPV11, HPV4, HPV17
## 58 HPV16, HPV11, HPV4, HPV17
## 59 HPV16, HPV11, HPV4, HPV17
## 60 HPV16, HPV11, HPV4, HPV17
## 61 HPV16, HPV11, HPV4, HPV17
## 62 HPV16, HPV11, HPV4, HPV17
## 63 HPV16, HPV11, HPV4, HPV17
## 64 HPV16, HPV11, HPV4, HPV17
## 65 HPV16, HPV11, HPV4, HPV17
## 66 HPV16, HPV11, HPV4, HPV17
## 67 HPV16, HPV11, HPV4, HPV17
## 68 HPV16, HPV11, HPV4, HPV17
## 69 HPV16, HPV11, HPV4, HPV17
## 70 HPV16, HPV11, HPV4, HPV17
## 71 HPV16, HPV11, HPV4, HPV17
## 72 HPV16, HPV11, HPV4, HPV17
## 73 HPV16, HPV11, HPV4, HPV17
## 74 HPV16, HPV11, HPV4, HPV17
## 75 HPV16, HPV11, HPV4, HPV17
## 76 HPV16, HPV11, HPV4, HPV17
## 77 HPV16, HPV11, HPV4, HPV17
## 78 HPV16, HPV11, HPV4, HPV17
## 79 HPV16, HPV11, HPV4, HPV17
## 80 HPV16, HPV11, HPV4, HPV17
## 81 HPV16, HPV11, HPV4, HPV17
## 82 HPV16, HPV11, HPV4, HPV17
## 83 HPV16, HPV11, HPV4, HPV17
## 84 HPV16, HPV11, HPV4, HPV17
## 85 HPV16, HPV11, HPV4, HPV17
## 86 HPV16, HPV11, HPV4, HPV17
## 87 HPV16, HPV11, HPV4, HPV17
## 88 HPV16, HPV11, HPV4, HPV17
## 89 HPV16, HPV11, HPV4, HPV17
## 90 HPV16, HPV11, HPV4, HPV17
## 91 HPV16, HPV11, HPV4, HPV17
## 92 HPV16, HPV11, HPV4, HPV17
## 93 HPV16, HPV11, HPV4, HPV17
## 94 HPV16, HPV11, HPV4, HPV17
## 95 HPV16, HPV11, HPV4, HPV17
## 96 HPV16, HPV11, HPV4, HPV17
## 97 HPV16, HPV11, HPV4, HPV17
## 98 HPV16, HPV11, HPV4, HPV17
## 99 HPV16, HPV11, HPV4, HPV17
## 100 HPV16, HPV11, HPV4, HPV17
## A DNAStringSet instance of length 31
## width seq names
## [1] 313 GGTATACATGGTACACATTATTA...ATATAGAGTATTTAGGGTGCAG gi|944543704|gb|K...
## [2] 312 TATACCGCATGCTGCATGCCATA...CACAAGTATAATATTAAGTATG gi|944543703|gb|K...
## [3] 316 ATTAGAGTTAATAAACACAGTTA...TTTAGCCAGTTCAAATTATTTT gi|944543701|gb|K...
## [4] 321 TATCACAGGGCGATTGCCCCCCT...ACAGGTATGCGTGCTTCACCTG gi|944543699|gb|K...
## [5] 313 CGGATGAATATGTTGCACGCACA...CTTTATTAAATAAATTGGATGA gi|944543697|gb|K...
## ... ... ...
## [27] 437 TTGAAGTACGGAATGGGCAGGAC...GTTAATAAACTCCATTATCGAA gi|440573440|gb|K...
## [28] 437 TTAATGTATATGAAGGTAACGAG...GTTAGTTAACAGCACTATTCAG gi|440573438|gb|K...
## [29] 440 ATGATGTCAGATCTAGTGATGGC...ATTAAAAAATACAGTAATTGAA gi|440573436|gb|K...
## [30] 437 TTGATGTTAGAGACACTGTGGAT...ATTAGTAAATACTGTAATTGAA gi|440573434|gb|K...
## [31] 440 TTGAAGTGCGTAATGGTTTGGGT...GTTAATAAATACAGTAATTGAA gi|440573432|gb|K...
## Adding 31 sequences to the database.
##
## 31 total sequences in table Seqs.
## Time difference of 0.03 secs
## Expression:
## alter table Seqs add column GI INTEGER
##
## Expression:
## update Seqs set GI = :GI where row_names = :row_names
##
## Expression:
## alter table Seqs add column SVAR INTEGER
##
## Expression:
## update Seqs set SVAR = :SVAR where row_names = :row_names
## Warning: Factors converted to character
## Expression:
## alter table Seqs add column ISO INTEGER
##
## Expression:
## update Seqs set ISO = :ISO where row_names = :row_names
##
## Expression:
## alter table Seqs add column GENE INTEGER
##
## Expression:
## update Seqs set GENE = :GENE where row_names = :row_names
## Warning: Factors converted to character
## Expression:
## update Seqs set identifier = :identifier where row_names = :row_names
## Warning: Factors converted to character
## Added to table Seqs: "GI" and "SVAR" and "ISO" and "GENE" and "identifier".
##
## Time difference of 0.02 secs
## row_names identifier
## 1 1 HPV18
## 2 2 HPV18
## 3 3 HPV16
## 4 4 HPV18
## description
## 1 gi|944543704|gb|KT365847.1| Human papillomavirus isolate HPV18-14 L1 protein gene, partial cds
## 2 gi|944543703|gb|KT365846.1| Human papillomavirus isolate HPV18-13 L1 protein gene, partial cds
## 3 gi|944543701|gb|KT365845.1| Human papillomavirus isolate HPV16-5 L1 protein gene, partial cds
## 4 gi|944543699|gb|KT365844.1| Human papillomavirus isolate HPV18-12 L1 protein gene, partial cds
## GI SVAR ISO GENE
## 1 944543704 HPV18 14 L1
## 2 944543703 HPV18 13 L1
## 3 944543701 HPV16 5 L1
## 4 944543699 HPV18 12 L1
data(RESTRICTION_ENZYMES)
FOCUS_ID <- 'HPV11'
TYPE <- 'melt'
LEVELS <- 4
MIN_LENGTH <- 15
MAX_LENGTH <- 25
MIN_SIZE <- 60
MAX_SIZE <- 200
RESOLUTION <- seq(75, 300, 15)
lapply(
rep(sample(1:3, 3), 3), # Random RE combinations
function(i)
DesignSignatures(
dbConn,
type = TYPE,
identifier = '',
focusID = FOCUS_ID,
enzymes = RESTRICTION_ENZYMES[i],
minProductSize = MIN_SIZE,
maxProductSize = MAX_SIZE,
resolution = RESOLUTION,
levels = LEVELS
)
) %>% print## Tallying 8-mers for 5 groups:
## ================================================================================
##
## Time difference of 0.39 secs
##
## Designing primer sequences based on the group 'HPV11':
## ================================================================================
##
## Time difference of 18.67 secs
##
## Selecting the most common primer sequences:
## ================================================================================
##
## Time difference of 3.85 secs
##
## Determining PCR products from each group:
## ================================================================================
##
## Time difference of 2.67 secs
##
## Scoring primer pair combinations:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Choosing optimal forward and reverse pairs:
## ================================================================================
##
## Time difference of 1.71 secs
##
## Finding the best restriction enzyme:
## ================================================================================
##
## Time difference of 2.39 secs
## Tallying 8-mers for 5 groups:
## ================================================================================
##
## Time difference of 0.36 secs
##
## Designing primer sequences based on the group 'HPV11':
## ================================================================================
##
## Time difference of 18.14 secs
##
## Selecting the most common primer sequences:
## ================================================================================
##
## Time difference of 4.1 secs
##
## Determining PCR products from each group:
## ================================================================================
##
## Time difference of 2.31 secs
##
## Scoring primer pair combinations:
## ================================================================================
##
## Time difference of 0.02 secs
##
## Choosing optimal forward and reverse pairs:
## ================================================================================
##
## Time difference of 1.69 secs
##
## Finding the best restriction enzyme:
## ================================================================================
##
## Time difference of 2.35 secs
## Tallying 8-mers for 5 groups:
## ================================================================================
##
## Time difference of 0.36 secs
##
## Designing primer sequences based on the group 'HPV11':
## ================================================================================
##
## Time difference of 18.32 secs
##
## Selecting the most common primer sequences:
## ================================================================================
##
## Time difference of 4.72 secs
##
## Determining PCR products from each group:
## ================================================================================
##
## Time difference of 2.84 secs
##
## Scoring primer pair combinations:
## ================================================================================
##
## Time difference of 0.02 secs
##
## Choosing optimal forward and reverse pairs:
## ================================================================================
##
## Time difference of 1.86 secs
##
## Finding the best restriction enzyme:
## ================================================================================
##
## Time difference of 2.15 secs
## Tallying 8-mers for 5 groups:
## ================================================================================
##
## Time difference of 0.4 secs
##
## Designing primer sequences based on the group 'HPV11':
## ================================================================================
##
## Time difference of 21.91 secs
##
## Selecting the most common primer sequences:
## ================================================================================
##
## Time difference of 4.9 secs
##
## Determining PCR products from each group:
## ================================================================================
##
## Time difference of 3.5 secs
##
## Scoring primer pair combinations:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Choosing optimal forward and reverse pairs:
## ================================================================================
##
## Time difference of 1.98 secs
##
## Finding the best restriction enzyme:
## ================================================================================
##
## Time difference of 2.97 secs
## Tallying 8-mers for 5 groups:
## ================================================================================
##
## Time difference of 0.58 secs
##
## Designing primer sequences based on the group 'HPV11':
## ================================================================================
##
## Time difference of 22.65 secs
##
## Selecting the most common primer sequences:
## ================================================================================
##
## Time difference of 4.64 secs
##
## Determining PCR products from each group:
## ================================================================================
##
## Time difference of 3.17 secs
##
## Scoring primer pair combinations:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Choosing optimal forward and reverse pairs:
## ================================================================================
##
## Time difference of 1.98 secs
##
## Finding the best restriction enzyme:
## ================================================================================
##
## Time difference of 2.36 secs
## Tallying 8-mers for 5 groups:
## ================================================================================
##
## Time difference of 0.4 secs
##
## Designing primer sequences based on the group 'HPV11':
## ================================================================================
##
## Time difference of 22.19 secs
##
## Selecting the most common primer sequences:
## ================================================================================
##
## Time difference of 3.7 secs
##
## Determining PCR products from each group:
## ================================================================================
##
## Time difference of 2.35 secs
##
## Scoring primer pair combinations:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Choosing optimal forward and reverse pairs:
## ================================================================================
##
## Time difference of 1.7 secs
##
## Finding the best restriction enzyme:
## ================================================================================
##
## Time difference of 2.28 secs
## Tallying 8-mers for 5 groups:
## ================================================================================
##
## Time difference of 0.34 secs
##
## Designing primer sequences based on the group 'HPV11':
## ================================================================================
##
## Time difference of 17.81 secs
##
## Selecting the most common primer sequences:
## ================================================================================
##
## Time difference of 4.07 secs
##
## Determining PCR products from each group:
## ================================================================================
##
## Time difference of 2.61 secs
##
## Scoring primer pair combinations:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Choosing optimal forward and reverse pairs:
## ================================================================================
##
## Time difference of 1.68 secs
##
## Finding the best restriction enzyme:
## ================================================================================
##
## Time difference of 1.94 secs
## Tallying 8-mers for 5 groups:
## ================================================================================
##
## Time difference of 0.35 secs
##
## Designing primer sequences based on the group 'HPV11':
## ================================================================================
##
## Time difference of 17.57 secs
##
## Selecting the most common primer sequences:
## ================================================================================
##
## Time difference of 3.96 secs
##
## Determining PCR products from each group:
## ================================================================================
##
## Time difference of 2.73 secs
##
## Scoring primer pair combinations:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Choosing optimal forward and reverse pairs:
## ================================================================================
##
## Time difference of 1.66 secs
##
## Finding the best restriction enzyme:
## ================================================================================
##
## Time difference of 1.93 secs
## Tallying 8-mers for 5 groups:
## ================================================================================
##
## Time difference of 0.36 secs
##
## Designing primer sequences based on the group 'HPV11':
## ================================================================================
##
## Time difference of 17.87 secs
##
## Selecting the most common primer sequences:
## ================================================================================
##
## Time difference of 3.94 secs
##
## Determining PCR products from each group:
## ================================================================================
##
## Time difference of 2.66 secs
##
## Scoring primer pair combinations:
## ================================================================================
##
## Time difference of 0.01 secs
##
## Choosing optimal forward and reverse pairs:
## ================================================================================
##
## Time difference of 1.71 secs
##
## Finding the best restriction enzyme:
## ================================================================================
##
## Time difference of 1.66 secs
## [[1]]
## forward_primer reverse_primer score coverage products
## 1 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 2 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 3 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGTT 0 0.2 0
## 4 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGT 0 0.2 0
## 5 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 6 GTTTGACCCCACTACACAGCG ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 7 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCT 0 0.2 0
## 8 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 9 GTTTGACCCCACTACACAGCG ACTAACACCAACGCCTAAAGGTTG 0 0.2 0
## 10 GTTTGACCCCACTACACAGCG CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 11 GTTTGACCCCACTACACAGCG CCACTAACRCCAACRCCTAAAGG 0 0.2 0
## 12 GTTTGACCCCACTACACAGCG GGATGCCCACTAACACCAACG 0 0.2 0
## 13 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAAG 0 0.2 0
## 14 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCTC 0 0.2 0
## 15 GTTTGACCCCACTACACAGCG GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 16 GTTTGACCCCACTACACAGCG TGCCCACTAACACCAACGC 0 0.2 0
## 17 GTTTGACCCCACTACACAGCG TGACCCCTGCCTACCTCC 0 0.2 0
## 18 GTTTGACCCCACTACACAGCG CAACGCCTAAAGGTTGACCCC 0 0.2 0
## 19 GTTTGACCCCACTACACAGCG CCAACGCCTAAAGGTTGACCC 0 0.2 0
## 20 GTTTGACCCCACTACACAGCG AGGTTGACCCCTGCCTACC 0 0.2 0
## 21 GTTTGACCCCACTACACAGCG ACCAACGCCTAAAGGTTGACC 0 0.2 0
## 22 GTTTGACCCCACTACACAGCG GCAATGGATGCCCACTAACACC 0 0.2 0
## 23 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 24 GTTTGACCCCACTACACAGCG ACACCAACGCCTAAAGGTTGAC 0 0.2 0
## 25 GTTTGACCCCACTACACAGCG AGCAATGGATGCCCACTAACAC 0 0.2 0
## 26 GTTTGACCCCACTACACAGCG TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 27 GTTTGACCCCACTACACAGCG ACCCCTGCCTACCTCCAAC 0 0.2 0
## 28 GTTTGACCCCACTACACAGCG ATGGATGCCCACTAACACCAAC 0 0.2 0
## 29 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 30 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTA 0 0.2 0
## 31 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 32 GTTTGACCCCACTACACAGCG CTAACACCAACGCCTAAAGGTTGA 0 0.2 0
## 33 GTTTGACCCCACTACACAGCG CACCYCTRCCTACCTCCA 0 0.2 0
## 34 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCA 0 0.2 0
## 35 GTTTGACCCCACTACACAGCG GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 36 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTAA 0 0.2 0
## 37 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 38 GTTTGACCCCACTACACAGCG GACCCCTGCCTACCTCCAA 0 0.2 0
## 39 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCAA 0 0.2 0
## 40 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAA 0 0.2 0
## 41 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 42 TGACCCCACTACACAGCGTT ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 43 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCT 0 0.2 0
## 44 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 45 TGACCCCACTACACAGCGTT CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 46 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCTC 0 0.2 0
## 47 TGACCCCACTACACAGCGTT GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 48 TGACCCCACTACACAGCGTT AGGTTGACCCCTGCCTACC 0 0.2 0
## 49 TGACCCCACTACACAGCGTT GCAATGGATGCCCACTAACACC 0 0.2 0
## 50 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 51 TGACCCCACTACACAGCGTT AGCAATGGATGCCCACTAACAC 0 0.2 0
## 52 TGACCCCACTACACAGCGTT TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 53 TGACCCCACTACACAGCGTT ATGGATGCCCACTAACACCAAC 0 0.2 0
## 54 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 55 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 56 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCA 0 0.2 0
## 57 TGACCCCACTACACAGCGTT GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 58 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 59 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCAA 0 0.2 0
## 60 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGT 0 0.2 0
## 61 TCCTTGCTGTGGGACATCCAT CACGCCCATACTAAACGCTGT 0 0.2 0
## 62 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGT 0 0.2 0
## 63 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGT 0 0.2 0
## 64 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAGT 0 0.2 0
## 65 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCT 0 0.2 0
## 66 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCT 0 0.2 0
## 67 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACT 0 0.2 0
## 68 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGAT 0 0.2 0
## 69 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGAAT 0 0.2 0
## 70 TCCTTGCTGTGGGACATCCAT ACGCCCATACTAAACGCTGTG 0 0.2 0
## 71 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGTG 0 0.2 0
## 72 TCCTTGCTGTGGGACATCCAT GCCCATACTAAACGCTGTGTAGTG 0 0.2 0
## 73 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCTG 0 0.2 0
## 74 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCTG 0 0.2 0
## 75 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGATG 0 0.2 0
## 76 TCCTTGCTGTGGGACATCCAT CATACTAAACGCTGTGTAGTGGGG 0 0.2 0
## 77 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGG 0 0.2 0
## 78 TCCTTGCTGTGGGACATCCAT CCTCCAACCCTGTGCACG 0 0.2 0
## 79 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAG 0 0.2 0
## 80 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGAG 0 0.2 0
## 81 TCCTTGCTGTGGGACATCCAT GTGGGGTCAAACAGAGATGAATCAG 0 0.2 0
## 82 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAG 0 0.2 0
## 83 TCCTTGCTGTGGGACATCCAT CTAAACGCTGTGTAGTGGGGTC 0 0.2 0
## 84 TCCTTGCTGTGGGACATCCAT GCCTACCTCCAACCCTGTGC 0 0.2 0
## 85 TCCTTGCTGTGGGACATCCAT TCCAACCCTGTGCACGC 0 0.2 0
## 86 TCCTTGCTGTGGGACATCCAT CCAACCCTGTGCACGCC 0 0.2 0
## 87 TCCTTGCTGTGGGACATCCAT CCCTGCCTACCTCCAACCC 0 0.2 0
## 88 TCCTTGCTGTGGGACATCCAT CCCCTGCCTACCTCCAACC 0 0.2 0
## 89 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATAC 0 0.2 0
## 90 TCCTTGCTGTGGGACATCCAT CCTACCTCCAACCCTGTGCAC 0 0.2 0
## 91 TCCTTGCTGTGGGACATCCAT ACCCCTGCCTACCTCCAAC 0 0.2 0
## 92 TCCTTGCTGTGGGACATCCAT CCTGTGCACGCCCATACTAAAC 0 0.2 0
## 93 TCCTTGCTGTGGGACATCCAT CGCTGTGTAGTGGGGTCAAAC 0 0.2 0
## 94 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTA 0 0.2 0
## 95 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGTA 0 0.2 0
## 96 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACTA 0 0.2 0
## 97 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATA 0 0.2 0
## 98 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGA 0 0.2 0
## 99 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGA 0 0.2 0
## 100 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGA 0 0.2 0
## similar_signatures missing_signatures enzyme digest_score fragments
## 1 HPV18, HPV16, HPV4, HPV17 Acc65I 0 2
## 2 HPV18, HPV16, HPV4, HPV17 Acc65I 0 2
## 3 HPV18, HPV16, HPV4, HPV17 0 0
## 4 HPV18, HPV16, HPV4, HPV17 0 0
## 5 HPV18, HPV16, HPV4, HPV17 0 0
## 6 HPV18, HPV16, HPV4, HPV17 0 0
## 7 HPV18, HPV16, HPV4, HPV17 0 0
## 8 HPV18, HPV16, HPV4, HPV17 0 0
## 9 HPV18, HPV16, HPV4, HPV17 0 0
## 10 HPV18, HPV16, HPV4, HPV17 0 0
## 11 HPV18, HPV16, HPV4, HPV17 0 0
## 12 HPV18, HPV16, HPV4, HPV17 0 0
## 13 HPV18, HPV16, HPV4, HPV17 0 0
## 14 HPV18, HPV16, HPV4, HPV17 0 0
## 15 HPV18, HPV16, HPV4, HPV17 0 0
## 16 HPV18, HPV16, HPV4, HPV17 0 0
## 17 HPV18, HPV16, HPV4, HPV17 0 0
## 18 HPV18, HPV16, HPV4, HPV17 0 0
## 19 HPV18, HPV16, HPV4, HPV17 0 0
## 20 HPV18, HPV16, HPV4, HPV17 0 0
## 21 HPV18, HPV16, HPV4, HPV17 0 0
## 22 HPV18, HPV16, HPV4, HPV17 0 0
## 23 HPV18, HPV16, HPV4, HPV17 0 0
## 24 HPV18, HPV16, HPV4, HPV17 0 0
## 25 HPV18, HPV16, HPV4, HPV17 0 0
## 26 HPV18, HPV16, HPV4, HPV17 0 0
## 27 HPV18, HPV16, HPV4, HPV17 0 0
## 28 HPV18, HPV16, HPV4, HPV17 0 0
## 29 HPV18, HPV16, HPV4, HPV17 0 0
## 30 HPV18, HPV16, HPV4, HPV17 0 0
## 31 HPV18, HPV16, HPV4, HPV17 0 0
## 32 HPV18, HPV16, HPV4, HPV17 0 0
## 33 HPV18, HPV16, HPV4, HPV17 0 0
## 34 HPV18, HPV16, HPV4, HPV17 0 0
## 35 HPV18, HPV16, HPV4, HPV17 0 0
## 36 HPV18, HPV16, HPV4, HPV17 0 0
## 37 HPV18, HPV16, HPV4, HPV17 0 0
## 38 HPV18, HPV16, HPV4, HPV17 0 0
## 39 HPV18, HPV16, HPV4, HPV17 0 0
## 40 HPV18, HPV16, HPV4, HPV17 0 0
## 41 HPV18, HPV16, HPV4, HPV17 0 0
## 42 HPV18, HPV16, HPV4, HPV17 0 0
## 43 HPV18, HPV16, HPV4, HPV17 0 0
## 44 HPV18, HPV16, HPV4, HPV17 0 0
## 45 HPV18, HPV16, HPV4, HPV17 0 0
## 46 HPV18, HPV16, HPV4, HPV17 0 0
## 47 HPV18, HPV16, HPV4, HPV17 0 0
## 48 HPV18, HPV16, HPV4, HPV17 0 0
## 49 HPV18, HPV16, HPV4, HPV17 0 0
## 50 HPV18, HPV16, HPV4, HPV17 0 0
## 51 HPV18, HPV16, HPV4, HPV17 0 0
## 52 HPV18, HPV16, HPV4, HPV17 0 0
## 53 HPV18, HPV16, HPV4, HPV17 0 0
## 54 HPV18, HPV16, HPV4, HPV17 0 0
## 55 HPV18, HPV16, HPV4, HPV17 0 0
## 56 HPV18, HPV16, HPV4, HPV17 0 0
## 57 HPV18, HPV16, HPV4, HPV17 0 0
## 58 HPV18, HPV16, HPV4, HPV17 0 0
## 59 HPV18, HPV16, HPV4, HPV17 0 0
## 60 HPV18, HPV16, HPV4, HPV17 0 0
## 61 HPV18, HPV16, HPV4, HPV17 0 0
## 62 HPV18, HPV16, HPV4, HPV17 0 0
## 63 HPV18, HPV16, HPV4, HPV17 0 0
## 64 HPV18, HPV16, HPV4, HPV17 0 0
## 65 HPV18, HPV16, HPV4, HPV17 0 0
## 66 HPV18, HPV16, HPV4, HPV17 0 0
## 67 HPV18, HPV16, HPV4, HPV17 0 0
## 68 HPV18, HPV16, HPV4, HPV17 0 0
## 69 HPV18, HPV16, HPV4, HPV17 0 0
## 70 HPV18, HPV16, HPV4, HPV17 0 0
## 71 HPV18, HPV16, HPV4, HPV17 0 0
## 72 HPV18, HPV16, HPV4, HPV17 0 0
## 73 HPV18, HPV16, HPV4, HPV17 0 0
## 74 HPV18, HPV16, HPV4, HPV17 0 0
## 75 HPV18, HPV16, HPV4, HPV17 0 0
## 76 HPV18, HPV16, HPV4, HPV17 0 0
## 77 HPV18, HPV16, HPV4, HPV17 0 0
## 78 HPV18, HPV16, HPV4, HPV17 0 0
## 79 HPV18, HPV16, HPV4, HPV17 0 0
## 80 HPV18, HPV16, HPV4, HPV17 0 0
## 81 HPV18, HPV16, HPV4, HPV17 0 0
## 82 HPV18, HPV16, HPV4, HPV17 0 0
## 83 HPV18, HPV16, HPV4, HPV17 0 0
## 84 HPV18, HPV16, HPV4, HPV17 0 0
## 85 HPV18, HPV16, HPV4, HPV17 0 0
## 86 HPV18, HPV16, HPV4, HPV17 0 0
## 87 HPV18, HPV16, HPV4, HPV17 0 0
## 88 HPV18, HPV16, HPV4, HPV17 0 0
## 89 HPV18, HPV16, HPV4, HPV17 0 0
## 90 HPV18, HPV16, HPV4, HPV17 0 0
## 91 HPV18, HPV16, HPV4, HPV17 0 0
## 92 HPV18, HPV16, HPV4, HPV17 0 0
## 93 HPV18, HPV16, HPV4, HPV17 0 0
## 94 HPV18, HPV16, HPV4, HPV17 0 0
## 95 HPV18, HPV16, HPV4, HPV17 0 0
## 96 HPV18, HPV16, HPV4, HPV17 0 0
## 97 HPV18, HPV16, HPV4, HPV17 0 0
## 98 HPV18, HPV16, HPV4, HPV17 0 0
## 99 HPV18, HPV16, HPV4, HPV17 0 0
## 100 HPV18, HPV16, HPV4, HPV17 0 0
##
## [[2]]
## forward_primer reverse_primer score coverage products
## 1 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGTT 0 0.2 0
## 2 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGT 0 0.2 0
## 3 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 4 GTTTGACCCCACTACACAGCG ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 5 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCT 0 0.2 0
## 6 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 7 GTTTGACCCCACTACACAGCG ACTAACACCAACGCCTAAAGGTTG 0 0.2 0
## 8 GTTTGACCCCACTACACAGCG CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 9 GTTTGACCCCACTACACAGCG CCACTAACRCCAACRCCTAAAGG 0 0.2 0
## 10 GTTTGACCCCACTACACAGCG GGATGCCCACTAACACCAACG 0 0.2 0
## 11 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAAG 0 0.2 0
## 12 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCTC 0 0.2 0
## 13 GTTTGACCCCACTACACAGCG GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 14 GTTTGACCCCACTACACAGCG TGCCCACTAACACCAACGC 0 0.2 0
## 15 GTTTGACCCCACTACACAGCG TGACCCCTGCCTACCTCC 0 0.2 0
## 16 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 17 GTTTGACCCCACTACACAGCG CAACGCCTAAAGGTTGACCCC 0 0.2 0
## 18 GTTTGACCCCACTACACAGCG CCAACGCCTAAAGGTTGACCC 0 0.2 0
## 19 GTTTGACCCCACTACACAGCG AGGTTGACCCCTGCCTACC 0 0.2 0
## 20 GTTTGACCCCACTACACAGCG ACCAACGCCTAAAGGTTGACC 0 0.2 0
## 21 GTTTGACCCCACTACACAGCG GCAATGGATGCCCACTAACACC 0 0.2 0
## 22 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 23 GTTTGACCCCACTACACAGCG ACACCAACGCCTAAAGGTTGAC 0 0.2 0
## 24 GTTTGACCCCACTACACAGCG AGCAATGGATGCCCACTAACAC 0 0.2 0
## 25 GTTTGACCCCACTACACAGCG TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 26 GTTTGACCCCACTACACAGCG ACCCCTGCCTACCTCCAAC 0 0.2 0
## 27 GTTTGACCCCACTACACAGCG ATGGATGCCCACTAACACCAAC 0 0.2 0
## 28 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 29 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTA 0 0.2 0
## 30 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 31 GTTTGACCCCACTACACAGCG CTAACACCAACGCCTAAAGGTTGA 0 0.2 0
## 32 GTTTGACCCCACTACACAGCG CACCYCTRCCTACCTCCA 0 0.2 0
## 33 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCA 0 0.2 0
## 34 GTTTGACCCCACTACACAGCG GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 35 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTAA 0 0.2 0
## 36 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 37 GTTTGACCCCACTACACAGCG GACCCCTGCCTACCTCCAA 0 0.2 0
## 38 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCAA 0 0.2 0
## 39 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAA 0 0.2 0
## 40 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 41 TGACCCCACTACACAGCGTT ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 42 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCT 0 0.2 0
## 43 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 44 TGACCCCACTACACAGCGTT CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 45 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCTC 0 0.2 0
## 46 TGACCCCACTACACAGCGTT GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 47 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 48 TGACCCCACTACACAGCGTT AGGTTGACCCCTGCCTACC 0 0.2 0
## 49 TGACCCCACTACACAGCGTT GCAATGGATGCCCACTAACACC 0 0.2 0
## 50 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 51 TGACCCCACTACACAGCGTT AGCAATGGATGCCCACTAACAC 0 0.2 0
## 52 TGACCCCACTACACAGCGTT TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 53 TGACCCCACTACACAGCGTT ATGGATGCCCACTAACACCAAC 0 0.2 0
## 54 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 55 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 56 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCA 0 0.2 0
## 57 TGACCCCACTACACAGCGTT GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 58 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 59 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCAA 0 0.2 0
## 60 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGT 0 0.2 0
## 61 TCCTTGCTGTGGGACATCCAT CACGCCCATACTAAACGCTGT 0 0.2 0
## 62 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGT 0 0.2 0
## 63 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGT 0 0.2 0
## 64 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAGT 0 0.2 0
## 65 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCT 0 0.2 0
## 66 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCT 0 0.2 0
## 67 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACT 0 0.2 0
## 68 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGAT 0 0.2 0
## 69 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGAAT 0 0.2 0
## 70 TCCTTGCTGTGGGACATCCAT ACGCCCATACTAAACGCTGTG 0 0.2 0
## 71 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGTG 0 0.2 0
## 72 TCCTTGCTGTGGGACATCCAT GCCCATACTAAACGCTGTGTAGTG 0 0.2 0
## 73 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCTG 0 0.2 0
## 74 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCTG 0 0.2 0
## 75 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGATG 0 0.2 0
## 76 TCCTTGCTGTGGGACATCCAT CATACTAAACGCTGTGTAGTGGGG 0 0.2 0
## 77 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGG 0 0.2 0
## 78 TCCTTGCTGTGGGACATCCAT CCTCCAACCCTGTGCACG 0 0.2 0
## 79 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAG 0 0.2 0
## 80 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGAG 0 0.2 0
## 81 TCCTTGCTGTGGGACATCCAT GTGGGGTCAAACAGAGATGAATCAG 0 0.2 0
## 82 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAG 0 0.2 0
## 83 TCCTTGCTGTGGGACATCCAT CTAAACGCTGTGTAGTGGGGTC 0 0.2 0
## 84 TCCTTGCTGTGGGACATCCAT GCCTACCTCCAACCCTGTGC 0 0.2 0
## 85 TCCTTGCTGTGGGACATCCAT TCCAACCCTGTGCACGC 0 0.2 0
## 86 TCCTTGCTGTGGGACATCCAT CCAACCCTGTGCACGCC 0 0.2 0
## 87 TCCTTGCTGTGGGACATCCAT CCCTGCCTACCTCCAACCC 0 0.2 0
## 88 TCCTTGCTGTGGGACATCCAT CCCCTGCCTACCTCCAACC 0 0.2 0
## 89 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATAC 0 0.2 0
## 90 TCCTTGCTGTGGGACATCCAT CCTACCTCCAACCCTGTGCAC 0 0.2 0
## 91 TCCTTGCTGTGGGACATCCAT ACCCCTGCCTACCTCCAAC 0 0.2 0
## 92 TCCTTGCTGTGGGACATCCAT CCTGTGCACGCCCATACTAAAC 0 0.2 0
## 93 TCCTTGCTGTGGGACATCCAT CGCTGTGTAGTGGGGTCAAAC 0 0.2 0
## 94 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTA 0 0.2 0
## 95 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGTA 0 0.2 0
## 96 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACTA 0 0.2 0
## 97 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATA 0 0.2 0
## 98 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGA 0 0.2 0
## 99 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGA 0 0.2 0
## 100 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGA 0 0.2 0
## similar_signatures missing_signatures enzyme digest_score fragments
## 1 HPV18, HPV16, HPV4, HPV17 0 0
## 2 HPV18, HPV16, HPV4, HPV17 0 0
## 3 HPV18, HPV16, HPV4, HPV17 0 0
## 4 HPV18, HPV16, HPV4, HPV17 0 0
## 5 HPV18, HPV16, HPV4, HPV17 0 0
## 6 HPV18, HPV16, HPV4, HPV17 0 0
## 7 HPV18, HPV16, HPV4, HPV17 0 0
## 8 HPV18, HPV16, HPV4, HPV17 0 0
## 9 HPV18, HPV16, HPV4, HPV17 0 0
## 10 HPV18, HPV16, HPV4, HPV17 0 0
## 11 HPV18, HPV16, HPV4, HPV17 0 0
## 12 HPV18, HPV16, HPV4, HPV17 0 0
## 13 HPV18, HPV16, HPV4, HPV17 0 0
## 14 HPV18, HPV16, HPV4, HPV17 0 0
## 15 HPV18, HPV16, HPV4, HPV17 0 0
## 16 HPV18, HPV16, HPV4, HPV17 0 0
## 17 HPV18, HPV16, HPV4, HPV17 0 0
## 18 HPV18, HPV16, HPV4, HPV17 0 0
## 19 HPV18, HPV16, HPV4, HPV17 0 0
## 20 HPV18, HPV16, HPV4, HPV17 0 0
## 21 HPV18, HPV16, HPV4, HPV17 0 0
## 22 HPV18, HPV16, HPV4, HPV17 0 0
## 23 HPV18, HPV16, HPV4, HPV17 0 0
## 24 HPV18, HPV16, HPV4, HPV17 0 0
## 25 HPV18, HPV16, HPV4, HPV17 0 0
## 26 HPV18, HPV16, HPV4, HPV17 0 0
## 27 HPV18, HPV16, HPV4, HPV17 0 0
## 28 HPV18, HPV16, HPV4, HPV17 0 0
## 29 HPV18, HPV16, HPV4, HPV17 0 0
## 30 HPV18, HPV16, HPV4, HPV17 0 0
## 31 HPV18, HPV16, HPV4, HPV17 0 0
## 32 HPV18, HPV16, HPV4, HPV17 0 0
## 33 HPV18, HPV16, HPV4, HPV17 0 0
## 34 HPV18, HPV16, HPV4, HPV17 0 0
## 35 HPV18, HPV16, HPV4, HPV17 0 0
## 36 HPV18, HPV16, HPV4, HPV17 0 0
## 37 HPV18, HPV16, HPV4, HPV17 0 0
## 38 HPV18, HPV16, HPV4, HPV17 0 0
## 39 HPV18, HPV16, HPV4, HPV17 0 0
## 40 HPV18, HPV16, HPV4, HPV17 0 0
## 41 HPV18, HPV16, HPV4, HPV17 0 0
## 42 HPV18, HPV16, HPV4, HPV17 0 0
## 43 HPV18, HPV16, HPV4, HPV17 0 0
## 44 HPV18, HPV16, HPV4, HPV17 0 0
## 45 HPV18, HPV16, HPV4, HPV17 0 0
## 46 HPV18, HPV16, HPV4, HPV17 0 0
## 47 HPV18, HPV16, HPV4, HPV17 0 0
## 48 HPV18, HPV16, HPV4, HPV17 0 0
## 49 HPV18, HPV16, HPV4, HPV17 0 0
## 50 HPV18, HPV16, HPV4, HPV17 0 0
## 51 HPV18, HPV16, HPV4, HPV17 0 0
## 52 HPV18, HPV16, HPV4, HPV17 0 0
## 53 HPV18, HPV16, HPV4, HPV17 0 0
## 54 HPV18, HPV16, HPV4, HPV17 0 0
## 55 HPV18, HPV16, HPV4, HPV17 0 0
## 56 HPV18, HPV16, HPV4, HPV17 0 0
## 57 HPV18, HPV16, HPV4, HPV17 0 0
## 58 HPV18, HPV16, HPV4, HPV17 0 0
## 59 HPV18, HPV16, HPV4, HPV17 0 0
## 60 HPV18, HPV16, HPV4, HPV17 0 0
## 61 HPV18, HPV16, HPV4, HPV17 0 0
## 62 HPV18, HPV16, HPV4, HPV17 0 0
## 63 HPV18, HPV16, HPV4, HPV17 0 0
## 64 HPV18, HPV16, HPV4, HPV17 0 0
## 65 HPV18, HPV16, HPV4, HPV17 0 0
## 66 HPV18, HPV16, HPV4, HPV17 0 0
## 67 HPV18, HPV16, HPV4, HPV17 0 0
## 68 HPV18, HPV16, HPV4, HPV17 0 0
## 69 HPV18, HPV16, HPV4, HPV17 0 0
## 70 HPV18, HPV16, HPV4, HPV17 0 0
## 71 HPV18, HPV16, HPV4, HPV17 0 0
## 72 HPV18, HPV16, HPV4, HPV17 0 0
## 73 HPV18, HPV16, HPV4, HPV17 0 0
## 74 HPV18, HPV16, HPV4, HPV17 0 0
## 75 HPV18, HPV16, HPV4, HPV17 0 0
## 76 HPV18, HPV16, HPV4, HPV17 0 0
## 77 HPV18, HPV16, HPV4, HPV17 0 0
## 78 HPV18, HPV16, HPV4, HPV17 0 0
## 79 HPV18, HPV16, HPV4, HPV17 0 0
## 80 HPV18, HPV16, HPV4, HPV17 0 0
## 81 HPV18, HPV16, HPV4, HPV17 0 0
## 82 HPV18, HPV16, HPV4, HPV17 0 0
## 83 HPV18, HPV16, HPV4, HPV17 0 0
## 84 HPV18, HPV16, HPV4, HPV17 0 0
## 85 HPV18, HPV16, HPV4, HPV17 0 0
## 86 HPV18, HPV16, HPV4, HPV17 0 0
## 87 HPV18, HPV16, HPV4, HPV17 0 0
## 88 HPV18, HPV16, HPV4, HPV17 0 0
## 89 HPV18, HPV16, HPV4, HPV17 0 0
## 90 HPV18, HPV16, HPV4, HPV17 0 0
## 91 HPV18, HPV16, HPV4, HPV17 0 0
## 92 HPV18, HPV16, HPV4, HPV17 0 0
## 93 HPV18, HPV16, HPV4, HPV17 0 0
## 94 HPV18, HPV16, HPV4, HPV17 0 0
## 95 HPV18, HPV16, HPV4, HPV17 0 0
## 96 HPV18, HPV16, HPV4, HPV17 0 0
## 97 HPV18, HPV16, HPV4, HPV17 0 0
## 98 HPV18, HPV16, HPV4, HPV17 0 0
## 99 HPV18, HPV16, HPV4, HPV17 0 0
## 100 HPV18, HPV16, HPV4, HPV17 0 0
##
## [[3]]
## forward_primer reverse_primer score coverage products
## 1 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGTT 0 0.2 0
## 2 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGT 0 0.2 0
## 3 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 4 GTTTGACCCCACTACACAGCG ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 5 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCT 0 0.2 0
## 6 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 7 GTTTGACCCCACTACACAGCG ACTAACACCAACGCCTAAAGGTTG 0 0.2 0
## 8 GTTTGACCCCACTACACAGCG CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 9 GTTTGACCCCACTACACAGCG CCACTAACRCCAACRCCTAAAGG 0 0.2 0
## 10 GTTTGACCCCACTACACAGCG GGATGCCCACTAACACCAACG 0 0.2 0
## 11 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAAG 0 0.2 0
## 12 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCTC 0 0.2 0
## 13 GTTTGACCCCACTACACAGCG GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 14 GTTTGACCCCACTACACAGCG TGCCCACTAACACCAACGC 0 0.2 0
## 15 GTTTGACCCCACTACACAGCG TGACCCCTGCCTACCTCC 0 0.2 0
## 16 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 17 GTTTGACCCCACTACACAGCG CAACGCCTAAAGGTTGACCCC 0 0.2 0
## 18 GTTTGACCCCACTACACAGCG CCAACGCCTAAAGGTTGACCC 0 0.2 0
## 19 GTTTGACCCCACTACACAGCG AGGTTGACCCCTGCCTACC 0 0.2 0
## 20 GTTTGACCCCACTACACAGCG ACCAACGCCTAAAGGTTGACC 0 0.2 0
## 21 GTTTGACCCCACTACACAGCG GCAATGGATGCCCACTAACACC 0 0.2 0
## 22 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 23 GTTTGACCCCACTACACAGCG ACACCAACGCCTAAAGGTTGAC 0 0.2 0
## 24 GTTTGACCCCACTACACAGCG AGCAATGGATGCCCACTAACAC 0 0.2 0
## 25 GTTTGACCCCACTACACAGCG TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 26 GTTTGACCCCACTACACAGCG ACCCCTGCCTACCTCCAAC 0 0.2 0
## 27 GTTTGACCCCACTACACAGCG ATGGATGCCCACTAACACCAAC 0 0.2 0
## 28 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 29 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTA 0 0.2 0
## 30 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 31 GTTTGACCCCACTACACAGCG CTAACACCAACGCCTAAAGGTTGA 0 0.2 0
## 32 GTTTGACCCCACTACACAGCG CACCYCTRCCTACCTCCA 0 0.2 0
## 33 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCA 0 0.2 0
## 34 GTTTGACCCCACTACACAGCG GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 35 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTAA 0 0.2 0
## 36 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 37 GTTTGACCCCACTACACAGCG GACCCCTGCCTACCTCCAA 0 0.2 0
## 38 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCAA 0 0.2 0
## 39 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAA 0 0.2 0
## 40 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 41 TGACCCCACTACACAGCGTT ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 42 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCT 0 0.2 0
## 43 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 44 TGACCCCACTACACAGCGTT CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 45 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCTC 0 0.2 0
## 46 TGACCCCACTACACAGCGTT GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 47 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 48 TGACCCCACTACACAGCGTT AGGTTGACCCCTGCCTACC 0 0.2 0
## 49 TGACCCCACTACACAGCGTT GCAATGGATGCCCACTAACACC 0 0.2 0
## 50 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 51 TGACCCCACTACACAGCGTT AGCAATGGATGCCCACTAACAC 0 0.2 0
## 52 TGACCCCACTACACAGCGTT TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 53 TGACCCCACTACACAGCGTT ATGGATGCCCACTAACACCAAC 0 0.2 0
## 54 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 55 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 56 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCA 0 0.2 0
## 57 TGACCCCACTACACAGCGTT GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 58 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 59 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCAA 0 0.2 0
## 60 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGT 0 0.2 0
## 61 TCCTTGCTGTGGGACATCCAT CACGCCCATACTAAACGCTGT 0 0.2 0
## 62 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGT 0 0.2 0
## 63 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGT 0 0.2 0
## 64 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAGT 0 0.2 0
## 65 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCT 0 0.2 0
## 66 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCT 0 0.2 0
## 67 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACT 0 0.2 0
## 68 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGAT 0 0.2 0
## 69 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGAAT 0 0.2 0
## 70 TCCTTGCTGTGGGACATCCAT ACGCCCATACTAAACGCTGTG 0 0.2 0
## 71 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGTG 0 0.2 0
## 72 TCCTTGCTGTGGGACATCCAT GCCCATACTAAACGCTGTGTAGTG 0 0.2 0
## 73 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCTG 0 0.2 0
## 74 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCTG 0 0.2 0
## 75 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGATG 0 0.2 0
## 76 TCCTTGCTGTGGGACATCCAT CATACTAAACGCTGTGTAGTGGGG 0 0.2 0
## 77 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGG 0 0.2 0
## 78 TCCTTGCTGTGGGACATCCAT CCTCCAACCCTGTGCACG 0 0.2 0
## 79 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAG 0 0.2 0
## 80 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGAG 0 0.2 0
## 81 TCCTTGCTGTGGGACATCCAT GTGGGGTCAAACAGAGATGAATCAG 0 0.2 0
## 82 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAG 0 0.2 0
## 83 TCCTTGCTGTGGGACATCCAT CTAAACGCTGTGTAGTGGGGTC 0 0.2 0
## 84 TCCTTGCTGTGGGACATCCAT GCCTACCTCCAACCCTGTGC 0 0.2 0
## 85 TCCTTGCTGTGGGACATCCAT TCCAACCCTGTGCACGC 0 0.2 0
## 86 TCCTTGCTGTGGGACATCCAT CCAACCCTGTGCACGCC 0 0.2 0
## 87 TCCTTGCTGTGGGACATCCAT CCCTGCCTACCTCCAACCC 0 0.2 0
## 88 TCCTTGCTGTGGGACATCCAT CCCCTGCCTACCTCCAACC 0 0.2 0
## 89 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATAC 0 0.2 0
## 90 TCCTTGCTGTGGGACATCCAT CCTACCTCCAACCCTGTGCAC 0 0.2 0
## 91 TCCTTGCTGTGGGACATCCAT ACCCCTGCCTACCTCCAAC 0 0.2 0
## 92 TCCTTGCTGTGGGACATCCAT CCTGTGCACGCCCATACTAAAC 0 0.2 0
## 93 TCCTTGCTGTGGGACATCCAT CGCTGTGTAGTGGGGTCAAAC 0 0.2 0
## 94 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTA 0 0.2 0
## 95 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGTA 0 0.2 0
## 96 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACTA 0 0.2 0
## 97 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATA 0 0.2 0
## 98 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGA 0 0.2 0
## 99 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGA 0 0.2 0
## 100 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGA 0 0.2 0
## similar_signatures missing_signatures enzyme digest_score fragments
## 1 HPV18, HPV16, HPV4, HPV17 0 0
## 2 HPV18, HPV16, HPV4, HPV17 0 0
## 3 HPV18, HPV16, HPV4, HPV17 0 0
## 4 HPV18, HPV16, HPV4, HPV17 0 0
## 5 HPV18, HPV16, HPV4, HPV17 0 0
## 6 HPV18, HPV16, HPV4, HPV17 0 0
## 7 HPV18, HPV16, HPV4, HPV17 0 0
## 8 HPV18, HPV16, HPV4, HPV17 0 0
## 9 HPV18, HPV16, HPV4, HPV17 0 0
## 10 HPV18, HPV16, HPV4, HPV17 0 0
## 11 HPV18, HPV16, HPV4, HPV17 0 0
## 12 HPV18, HPV16, HPV4, HPV17 0 0
## 13 HPV18, HPV16, HPV4, HPV17 0 0
## 14 HPV18, HPV16, HPV4, HPV17 0 0
## 15 HPV18, HPV16, HPV4, HPV17 0 0
## 16 HPV18, HPV16, HPV4, HPV17 0 0
## 17 HPV18, HPV16, HPV4, HPV17 0 0
## 18 HPV18, HPV16, HPV4, HPV17 0 0
## 19 HPV18, HPV16, HPV4, HPV17 0 0
## 20 HPV18, HPV16, HPV4, HPV17 0 0
## 21 HPV18, HPV16, HPV4, HPV17 0 0
## 22 HPV18, HPV16, HPV4, HPV17 0 0
## 23 HPV18, HPV16, HPV4, HPV17 0 0
## 24 HPV18, HPV16, HPV4, HPV17 0 0
## 25 HPV18, HPV16, HPV4, HPV17 0 0
## 26 HPV18, HPV16, HPV4, HPV17 0 0
## 27 HPV18, HPV16, HPV4, HPV17 0 0
## 28 HPV18, HPV16, HPV4, HPV17 0 0
## 29 HPV18, HPV16, HPV4, HPV17 0 0
## 30 HPV18, HPV16, HPV4, HPV17 0 0
## 31 HPV18, HPV16, HPV4, HPV17 0 0
## 32 HPV18, HPV16, HPV4, HPV17 0 0
## 33 HPV18, HPV16, HPV4, HPV17 0 0
## 34 HPV18, HPV16, HPV4, HPV17 0 0
## 35 HPV18, HPV16, HPV4, HPV17 0 0
## 36 HPV18, HPV16, HPV4, HPV17 0 0
## 37 HPV18, HPV16, HPV4, HPV17 0 0
## 38 HPV18, HPV16, HPV4, HPV17 0 0
## 39 HPV18, HPV16, HPV4, HPV17 0 0
## 40 HPV18, HPV16, HPV4, HPV17 0 0
## 41 HPV18, HPV16, HPV4, HPV17 0 0
## 42 HPV18, HPV16, HPV4, HPV17 0 0
## 43 HPV18, HPV16, HPV4, HPV17 0 0
## 44 HPV18, HPV16, HPV4, HPV17 0 0
## 45 HPV18, HPV16, HPV4, HPV17 0 0
## 46 HPV18, HPV16, HPV4, HPV17 0 0
## 47 HPV18, HPV16, HPV4, HPV17 0 0
## 48 HPV18, HPV16, HPV4, HPV17 0 0
## 49 HPV18, HPV16, HPV4, HPV17 0 0
## 50 HPV18, HPV16, HPV4, HPV17 0 0
## 51 HPV18, HPV16, HPV4, HPV17 0 0
## 52 HPV18, HPV16, HPV4, HPV17 0 0
## 53 HPV18, HPV16, HPV4, HPV17 0 0
## 54 HPV18, HPV16, HPV4, HPV17 0 0
## 55 HPV18, HPV16, HPV4, HPV17 0 0
## 56 HPV18, HPV16, HPV4, HPV17 0 0
## 57 HPV18, HPV16, HPV4, HPV17 0 0
## 58 HPV18, HPV16, HPV4, HPV17 0 0
## 59 HPV18, HPV16, HPV4, HPV17 0 0
## 60 HPV18, HPV16, HPV4, HPV17 0 0
## 61 HPV18, HPV16, HPV4, HPV17 0 0
## 62 HPV18, HPV16, HPV4, HPV17 0 0
## 63 HPV18, HPV16, HPV4, HPV17 0 0
## 64 HPV18, HPV16, HPV4, HPV17 0 0
## 65 HPV18, HPV16, HPV4, HPV17 0 0
## 66 HPV18, HPV16, HPV4, HPV17 0 0
## 67 HPV18, HPV16, HPV4, HPV17 0 0
## 68 HPV18, HPV16, HPV4, HPV17 0 0
## 69 HPV18, HPV16, HPV4, HPV17 0 0
## 70 HPV18, HPV16, HPV4, HPV17 0 0
## 71 HPV18, HPV16, HPV4, HPV17 0 0
## 72 HPV18, HPV16, HPV4, HPV17 0 0
## 73 HPV18, HPV16, HPV4, HPV17 0 0
## 74 HPV18, HPV16, HPV4, HPV17 0 0
## 75 HPV18, HPV16, HPV4, HPV17 0 0
## 76 HPV18, HPV16, HPV4, HPV17 0 0
## 77 HPV18, HPV16, HPV4, HPV17 0 0
## 78 HPV18, HPV16, HPV4, HPV17 0 0
## 79 HPV18, HPV16, HPV4, HPV17 0 0
## 80 HPV18, HPV16, HPV4, HPV17 0 0
## 81 HPV18, HPV16, HPV4, HPV17 0 0
## 82 HPV18, HPV16, HPV4, HPV17 0 0
## 83 HPV18, HPV16, HPV4, HPV17 0 0
## 84 HPV18, HPV16, HPV4, HPV17 0 0
## 85 HPV18, HPV16, HPV4, HPV17 0 0
## 86 HPV18, HPV16, HPV4, HPV17 0 0
## 87 HPV18, HPV16, HPV4, HPV17 0 0
## 88 HPV18, HPV16, HPV4, HPV17 0 0
## 89 HPV18, HPV16, HPV4, HPV17 0 0
## 90 HPV18, HPV16, HPV4, HPV17 0 0
## 91 HPV18, HPV16, HPV4, HPV17 0 0
## 92 HPV18, HPV16, HPV4, HPV17 0 0
## 93 HPV18, HPV16, HPV4, HPV17 0 0
## 94 HPV18, HPV16, HPV4, HPV17 0 0
## 95 HPV18, HPV16, HPV4, HPV17 0 0
## 96 HPV18, HPV16, HPV4, HPV17 0 0
## 97 HPV18, HPV16, HPV4, HPV17 0 0
## 98 HPV18, HPV16, HPV4, HPV17 0 0
## 99 HPV18, HPV16, HPV4, HPV17 0 0
## 100 HPV18, HPV16, HPV4, HPV17 0 0
##
## [[4]]
## forward_primer reverse_primer score coverage products
## 1 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 2 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 3 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGTT 0 0.2 0
## 4 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGT 0 0.2 0
## 5 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 6 GTTTGACCCCACTACACAGCG ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 7 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCT 0 0.2 0
## 8 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 9 GTTTGACCCCACTACACAGCG ACTAACACCAACGCCTAAAGGTTG 0 0.2 0
## 10 GTTTGACCCCACTACACAGCG CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 11 GTTTGACCCCACTACACAGCG CCACTAACRCCAACRCCTAAAGG 0 0.2 0
## 12 GTTTGACCCCACTACACAGCG GGATGCCCACTAACACCAACG 0 0.2 0
## 13 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAAG 0 0.2 0
## 14 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCTC 0 0.2 0
## 15 GTTTGACCCCACTACACAGCG GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 16 GTTTGACCCCACTACACAGCG TGCCCACTAACACCAACGC 0 0.2 0
## 17 GTTTGACCCCACTACACAGCG TGACCCCTGCCTACCTCC 0 0.2 0
## 18 GTTTGACCCCACTACACAGCG CAACGCCTAAAGGTTGACCCC 0 0.2 0
## 19 GTTTGACCCCACTACACAGCG CCAACGCCTAAAGGTTGACCC 0 0.2 0
## 20 GTTTGACCCCACTACACAGCG AGGTTGACCCCTGCCTACC 0 0.2 0
## 21 GTTTGACCCCACTACACAGCG ACCAACGCCTAAAGGTTGACC 0 0.2 0
## 22 GTTTGACCCCACTACACAGCG GCAATGGATGCCCACTAACACC 0 0.2 0
## 23 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 24 GTTTGACCCCACTACACAGCG ACACCAACGCCTAAAGGTTGAC 0 0.2 0
## 25 GTTTGACCCCACTACACAGCG AGCAATGGATGCCCACTAACAC 0 0.2 0
## 26 GTTTGACCCCACTACACAGCG TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 27 GTTTGACCCCACTACACAGCG ACCCCTGCCTACCTCCAAC 0 0.2 0
## 28 GTTTGACCCCACTACACAGCG ATGGATGCCCACTAACACCAAC 0 0.2 0
## 29 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 30 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTA 0 0.2 0
## 31 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 32 GTTTGACCCCACTACACAGCG CTAACACCAACGCCTAAAGGTTGA 0 0.2 0
## 33 GTTTGACCCCACTACACAGCG CACCYCTRCCTACCTCCA 0 0.2 0
## 34 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCA 0 0.2 0
## 35 GTTTGACCCCACTACACAGCG GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 36 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTAA 0 0.2 0
## 37 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 38 GTTTGACCCCACTACACAGCG GACCCCTGCCTACCTCCAA 0 0.2 0
## 39 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCAA 0 0.2 0
## 40 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAA 0 0.2 0
## 41 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 42 TGACCCCACTACACAGCGTT ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 43 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCT 0 0.2 0
## 44 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 45 TGACCCCACTACACAGCGTT CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 46 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCTC 0 0.2 0
## 47 TGACCCCACTACACAGCGTT GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 48 TGACCCCACTACACAGCGTT AGGTTGACCCCTGCCTACC 0 0.2 0
## 49 TGACCCCACTACACAGCGTT GCAATGGATGCCCACTAACACC 0 0.2 0
## 50 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 51 TGACCCCACTACACAGCGTT AGCAATGGATGCCCACTAACAC 0 0.2 0
## 52 TGACCCCACTACACAGCGTT TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 53 TGACCCCACTACACAGCGTT ATGGATGCCCACTAACACCAAC 0 0.2 0
## 54 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 55 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 56 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCA 0 0.2 0
## 57 TGACCCCACTACACAGCGTT GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 58 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 59 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCAA 0 0.2 0
## 60 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGT 0 0.2 0
## 61 TCCTTGCTGTGGGACATCCAT CACGCCCATACTAAACGCTGT 0 0.2 0
## 62 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGT 0 0.2 0
## 63 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGT 0 0.2 0
## 64 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAGT 0 0.2 0
## 65 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCT 0 0.2 0
## 66 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCT 0 0.2 0
## 67 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACT 0 0.2 0
## 68 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGAT 0 0.2 0
## 69 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGAAT 0 0.2 0
## 70 TCCTTGCTGTGGGACATCCAT ACGCCCATACTAAACGCTGTG 0 0.2 0
## 71 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGTG 0 0.2 0
## 72 TCCTTGCTGTGGGACATCCAT GCCCATACTAAACGCTGTGTAGTG 0 0.2 0
## 73 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCTG 0 0.2 0
## 74 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCTG 0 0.2 0
## 75 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGATG 0 0.2 0
## 76 TCCTTGCTGTGGGACATCCAT CATACTAAACGCTGTGTAGTGGGG 0 0.2 0
## 77 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGG 0 0.2 0
## 78 TCCTTGCTGTGGGACATCCAT CCTCCAACCCTGTGCACG 0 0.2 0
## 79 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAG 0 0.2 0
## 80 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGAG 0 0.2 0
## 81 TCCTTGCTGTGGGACATCCAT GTGGGGTCAAACAGAGATGAATCAG 0 0.2 0
## 82 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAG 0 0.2 0
## 83 TCCTTGCTGTGGGACATCCAT CTAAACGCTGTGTAGTGGGGTC 0 0.2 0
## 84 TCCTTGCTGTGGGACATCCAT GCCTACCTCCAACCCTGTGC 0 0.2 0
## 85 TCCTTGCTGTGGGACATCCAT TCCAACCCTGTGCACGC 0 0.2 0
## 86 TCCTTGCTGTGGGACATCCAT CCAACCCTGTGCACGCC 0 0.2 0
## 87 TCCTTGCTGTGGGACATCCAT CCCTGCCTACCTCCAACCC 0 0.2 0
## 88 TCCTTGCTGTGGGACATCCAT CCCCTGCCTACCTCCAACC 0 0.2 0
## 89 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATAC 0 0.2 0
## 90 TCCTTGCTGTGGGACATCCAT CCTACCTCCAACCCTGTGCAC 0 0.2 0
## 91 TCCTTGCTGTGGGACATCCAT ACCCCTGCCTACCTCCAAC 0 0.2 0
## 92 TCCTTGCTGTGGGACATCCAT CCTGTGCACGCCCATACTAAAC 0 0.2 0
## 93 TCCTTGCTGTGGGACATCCAT CGCTGTGTAGTGGGGTCAAAC 0 0.2 0
## 94 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTA 0 0.2 0
## 95 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGTA 0 0.2 0
## 96 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACTA 0 0.2 0
## 97 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATA 0 0.2 0
## 98 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGA 0 0.2 0
## 99 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGA 0 0.2 0
## 100 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGA 0 0.2 0
## similar_signatures missing_signatures enzyme digest_score fragments
## 1 HPV18, HPV16, HPV4, HPV17 Acc65I 0 2
## 2 HPV18, HPV16, HPV4, HPV17 Acc65I 0 2
## 3 HPV18, HPV16, HPV4, HPV17 0 0
## 4 HPV18, HPV16, HPV4, HPV17 0 0
## 5 HPV18, HPV16, HPV4, HPV17 0 0
## 6 HPV18, HPV16, HPV4, HPV17 0 0
## 7 HPV18, HPV16, HPV4, HPV17 0 0
## 8 HPV18, HPV16, HPV4, HPV17 0 0
## 9 HPV18, HPV16, HPV4, HPV17 0 0
## 10 HPV18, HPV16, HPV4, HPV17 0 0
## 11 HPV18, HPV16, HPV4, HPV17 0 0
## 12 HPV18, HPV16, HPV4, HPV17 0 0
## 13 HPV18, HPV16, HPV4, HPV17 0 0
## 14 HPV18, HPV16, HPV4, HPV17 0 0
## 15 HPV18, HPV16, HPV4, HPV17 0 0
## 16 HPV18, HPV16, HPV4, HPV17 0 0
## 17 HPV18, HPV16, HPV4, HPV17 0 0
## 18 HPV18, HPV16, HPV4, HPV17 0 0
## 19 HPV18, HPV16, HPV4, HPV17 0 0
## 20 HPV18, HPV16, HPV4, HPV17 0 0
## 21 HPV18, HPV16, HPV4, HPV17 0 0
## 22 HPV18, HPV16, HPV4, HPV17 0 0
## 23 HPV18, HPV16, HPV4, HPV17 0 0
## 24 HPV18, HPV16, HPV4, HPV17 0 0
## 25 HPV18, HPV16, HPV4, HPV17 0 0
## 26 HPV18, HPV16, HPV4, HPV17 0 0
## 27 HPV18, HPV16, HPV4, HPV17 0 0
## 28 HPV18, HPV16, HPV4, HPV17 0 0
## 29 HPV18, HPV16, HPV4, HPV17 0 0
## 30 HPV18, HPV16, HPV4, HPV17 0 0
## 31 HPV18, HPV16, HPV4, HPV17 0 0
## 32 HPV18, HPV16, HPV4, HPV17 0 0
## 33 HPV18, HPV16, HPV4, HPV17 0 0
## 34 HPV18, HPV16, HPV4, HPV17 0 0
## 35 HPV18, HPV16, HPV4, HPV17 0 0
## 36 HPV18, HPV16, HPV4, HPV17 0 0
## 37 HPV18, HPV16, HPV4, HPV17 0 0
## 38 HPV18, HPV16, HPV4, HPV17 0 0
## 39 HPV18, HPV16, HPV4, HPV17 0 0
## 40 HPV18, HPV16, HPV4, HPV17 0 0
## 41 HPV18, HPV16, HPV4, HPV17 0 0
## 42 HPV18, HPV16, HPV4, HPV17 0 0
## 43 HPV18, HPV16, HPV4, HPV17 0 0
## 44 HPV18, HPV16, HPV4, HPV17 0 0
## 45 HPV18, HPV16, HPV4, HPV17 0 0
## 46 HPV18, HPV16, HPV4, HPV17 0 0
## 47 HPV18, HPV16, HPV4, HPV17 0 0
## 48 HPV18, HPV16, HPV4, HPV17 0 0
## 49 HPV18, HPV16, HPV4, HPV17 0 0
## 50 HPV18, HPV16, HPV4, HPV17 0 0
## 51 HPV18, HPV16, HPV4, HPV17 0 0
## 52 HPV18, HPV16, HPV4, HPV17 0 0
## 53 HPV18, HPV16, HPV4, HPV17 0 0
## 54 HPV18, HPV16, HPV4, HPV17 0 0
## 55 HPV18, HPV16, HPV4, HPV17 0 0
## 56 HPV18, HPV16, HPV4, HPV17 0 0
## 57 HPV18, HPV16, HPV4, HPV17 0 0
## 58 HPV18, HPV16, HPV4, HPV17 0 0
## 59 HPV18, HPV16, HPV4, HPV17 0 0
## 60 HPV18, HPV16, HPV4, HPV17 0 0
## 61 HPV18, HPV16, HPV4, HPV17 0 0
## 62 HPV18, HPV16, HPV4, HPV17 0 0
## 63 HPV18, HPV16, HPV4, HPV17 0 0
## 64 HPV18, HPV16, HPV4, HPV17 0 0
## 65 HPV18, HPV16, HPV4, HPV17 0 0
## 66 HPV18, HPV16, HPV4, HPV17 0 0
## 67 HPV18, HPV16, HPV4, HPV17 0 0
## 68 HPV18, HPV16, HPV4, HPV17 0 0
## 69 HPV18, HPV16, HPV4, HPV17 0 0
## 70 HPV18, HPV16, HPV4, HPV17 0 0
## 71 HPV18, HPV16, HPV4, HPV17 0 0
## 72 HPV18, HPV16, HPV4, HPV17 0 0
## 73 HPV18, HPV16, HPV4, HPV17 0 0
## 74 HPV18, HPV16, HPV4, HPV17 0 0
## 75 HPV18, HPV16, HPV4, HPV17 0 0
## 76 HPV18, HPV16, HPV4, HPV17 0 0
## 77 HPV18, HPV16, HPV4, HPV17 0 0
## 78 HPV18, HPV16, HPV4, HPV17 0 0
## 79 HPV18, HPV16, HPV4, HPV17 0 0
## 80 HPV18, HPV16, HPV4, HPV17 0 0
## 81 HPV18, HPV16, HPV4, HPV17 0 0
## 82 HPV18, HPV16, HPV4, HPV17 0 0
## 83 HPV18, HPV16, HPV4, HPV17 0 0
## 84 HPV18, HPV16, HPV4, HPV17 0 0
## 85 HPV18, HPV16, HPV4, HPV17 0 0
## 86 HPV18, HPV16, HPV4, HPV17 0 0
## 87 HPV18, HPV16, HPV4, HPV17 0 0
## 88 HPV18, HPV16, HPV4, HPV17 0 0
## 89 HPV18, HPV16, HPV4, HPV17 0 0
## 90 HPV18, HPV16, HPV4, HPV17 0 0
## 91 HPV18, HPV16, HPV4, HPV17 0 0
## 92 HPV18, HPV16, HPV4, HPV17 0 0
## 93 HPV18, HPV16, HPV4, HPV17 0 0
## 94 HPV18, HPV16, HPV4, HPV17 0 0
## 95 HPV18, HPV16, HPV4, HPV17 0 0
## 96 HPV18, HPV16, HPV4, HPV17 0 0
## 97 HPV18, HPV16, HPV4, HPV17 0 0
## 98 HPV18, HPV16, HPV4, HPV17 0 0
## 99 HPV18, HPV16, HPV4, HPV17 0 0
## 100 HPV18, HPV16, HPV4, HPV17 0 0
##
## [[5]]
## forward_primer reverse_primer score coverage products
## 1 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGTT 0 0.2 0
## 2 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGT 0 0.2 0
## 3 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 4 GTTTGACCCCACTACACAGCG ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 5 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCT 0 0.2 0
## 6 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 7 GTTTGACCCCACTACACAGCG ACTAACACCAACGCCTAAAGGTTG 0 0.2 0
## 8 GTTTGACCCCACTACACAGCG CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 9 GTTTGACCCCACTACACAGCG CCACTAACRCCAACRCCTAAAGG 0 0.2 0
## 10 GTTTGACCCCACTACACAGCG GGATGCCCACTAACACCAACG 0 0.2 0
## 11 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAAG 0 0.2 0
## 12 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCTC 0 0.2 0
## 13 GTTTGACCCCACTACACAGCG GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 14 GTTTGACCCCACTACACAGCG TGCCCACTAACACCAACGC 0 0.2 0
## 15 GTTTGACCCCACTACACAGCG TGACCCCTGCCTACCTCC 0 0.2 0
## 16 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 17 GTTTGACCCCACTACACAGCG CAACGCCTAAAGGTTGACCCC 0 0.2 0
## 18 GTTTGACCCCACTACACAGCG CCAACGCCTAAAGGTTGACCC 0 0.2 0
## 19 GTTTGACCCCACTACACAGCG AGGTTGACCCCTGCCTACC 0 0.2 0
## 20 GTTTGACCCCACTACACAGCG ACCAACGCCTAAAGGTTGACC 0 0.2 0
## 21 GTTTGACCCCACTACACAGCG GCAATGGATGCCCACTAACACC 0 0.2 0
## 22 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 23 GTTTGACCCCACTACACAGCG ACACCAACGCCTAAAGGTTGAC 0 0.2 0
## 24 GTTTGACCCCACTACACAGCG AGCAATGGATGCCCACTAACAC 0 0.2 0
## 25 GTTTGACCCCACTACACAGCG TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 26 GTTTGACCCCACTACACAGCG ACCCCTGCCTACCTCCAAC 0 0.2 0
## 27 GTTTGACCCCACTACACAGCG ATGGATGCCCACTAACACCAAC 0 0.2 0
## 28 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 29 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTA 0 0.2 0
## 30 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 31 GTTTGACCCCACTACACAGCG CTAACACCAACGCCTAAAGGTTGA 0 0.2 0
## 32 GTTTGACCCCACTACACAGCG CACCYCTRCCTACCTCCA 0 0.2 0
## 33 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCA 0 0.2 0
## 34 GTTTGACCCCACTACACAGCG GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 35 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTAA 0 0.2 0
## 36 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 37 GTTTGACCCCACTACACAGCG GACCCCTGCCTACCTCCAA 0 0.2 0
## 38 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCAA 0 0.2 0
## 39 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAA 0 0.2 0
## 40 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 41 TGACCCCACTACACAGCGTT ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 42 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCT 0 0.2 0
## 43 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 44 TGACCCCACTACACAGCGTT CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 45 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCTC 0 0.2 0
## 46 TGACCCCACTACACAGCGTT GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 47 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 48 TGACCCCACTACACAGCGTT AGGTTGACCCCTGCCTACC 0 0.2 0
## 49 TGACCCCACTACACAGCGTT GCAATGGATGCCCACTAACACC 0 0.2 0
## 50 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 51 TGACCCCACTACACAGCGTT AGCAATGGATGCCCACTAACAC 0 0.2 0
## 52 TGACCCCACTACACAGCGTT TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 53 TGACCCCACTACACAGCGTT ATGGATGCCCACTAACACCAAC 0 0.2 0
## 54 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 55 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 56 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCA 0 0.2 0
## 57 TGACCCCACTACACAGCGTT GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 58 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 59 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCAA 0 0.2 0
## 60 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGT 0 0.2 0
## 61 TCCTTGCTGTGGGACATCCAT CACGCCCATACTAAACGCTGT 0 0.2 0
## 62 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGT 0 0.2 0
## 63 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGT 0 0.2 0
## 64 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAGT 0 0.2 0
## 65 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCT 0 0.2 0
## 66 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCT 0 0.2 0
## 67 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACT 0 0.2 0
## 68 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGAT 0 0.2 0
## 69 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGAAT 0 0.2 0
## 70 TCCTTGCTGTGGGACATCCAT ACGCCCATACTAAACGCTGTG 0 0.2 0
## 71 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGTG 0 0.2 0
## 72 TCCTTGCTGTGGGACATCCAT GCCCATACTAAACGCTGTGTAGTG 0 0.2 0
## 73 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCTG 0 0.2 0
## 74 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCTG 0 0.2 0
## 75 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGATG 0 0.2 0
## 76 TCCTTGCTGTGGGACATCCAT CATACTAAACGCTGTGTAGTGGGG 0 0.2 0
## 77 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGG 0 0.2 0
## 78 TCCTTGCTGTGGGACATCCAT CCTCCAACCCTGTGCACG 0 0.2 0
## 79 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAG 0 0.2 0
## 80 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGAG 0 0.2 0
## 81 TCCTTGCTGTGGGACATCCAT GTGGGGTCAAACAGAGATGAATCAG 0 0.2 0
## 82 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAG 0 0.2 0
## 83 TCCTTGCTGTGGGACATCCAT CTAAACGCTGTGTAGTGGGGTC 0 0.2 0
## 84 TCCTTGCTGTGGGACATCCAT GCCTACCTCCAACCCTGTGC 0 0.2 0
## 85 TCCTTGCTGTGGGACATCCAT TCCAACCCTGTGCACGC 0 0.2 0
## 86 TCCTTGCTGTGGGACATCCAT CCAACCCTGTGCACGCC 0 0.2 0
## 87 TCCTTGCTGTGGGACATCCAT CCCTGCCTACCTCCAACCC 0 0.2 0
## 88 TCCTTGCTGTGGGACATCCAT CCCCTGCCTACCTCCAACC 0 0.2 0
## 89 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATAC 0 0.2 0
## 90 TCCTTGCTGTGGGACATCCAT CCTACCTCCAACCCTGTGCAC 0 0.2 0
## 91 TCCTTGCTGTGGGACATCCAT ACCCCTGCCTACCTCCAAC 0 0.2 0
## 92 TCCTTGCTGTGGGACATCCAT CCTGTGCACGCCCATACTAAAC 0 0.2 0
## 93 TCCTTGCTGTGGGACATCCAT CGCTGTGTAGTGGGGTCAAAC 0 0.2 0
## 94 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTA 0 0.2 0
## 95 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGTA 0 0.2 0
## 96 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACTA 0 0.2 0
## 97 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATA 0 0.2 0
## 98 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGA 0 0.2 0
## 99 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGA 0 0.2 0
## 100 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGA 0 0.2 0
## similar_signatures missing_signatures enzyme digest_score fragments
## 1 HPV18, HPV16, HPV4, HPV17 0 0
## 2 HPV18, HPV16, HPV4, HPV17 0 0
## 3 HPV18, HPV16, HPV4, HPV17 0 0
## 4 HPV18, HPV16, HPV4, HPV17 0 0
## 5 HPV18, HPV16, HPV4, HPV17 0 0
## 6 HPV18, HPV16, HPV4, HPV17 0 0
## 7 HPV18, HPV16, HPV4, HPV17 0 0
## 8 HPV18, HPV16, HPV4, HPV17 0 0
## 9 HPV18, HPV16, HPV4, HPV17 0 0
## 10 HPV18, HPV16, HPV4, HPV17 0 0
## 11 HPV18, HPV16, HPV4, HPV17 0 0
## 12 HPV18, HPV16, HPV4, HPV17 0 0
## 13 HPV18, HPV16, HPV4, HPV17 0 0
## 14 HPV18, HPV16, HPV4, HPV17 0 0
## 15 HPV18, HPV16, HPV4, HPV17 0 0
## 16 HPV18, HPV16, HPV4, HPV17 0 0
## 17 HPV18, HPV16, HPV4, HPV17 0 0
## 18 HPV18, HPV16, HPV4, HPV17 0 0
## 19 HPV18, HPV16, HPV4, HPV17 0 0
## 20 HPV18, HPV16, HPV4, HPV17 0 0
## 21 HPV18, HPV16, HPV4, HPV17 0 0
## 22 HPV18, HPV16, HPV4, HPV17 0 0
## 23 HPV18, HPV16, HPV4, HPV17 0 0
## 24 HPV18, HPV16, HPV4, HPV17 0 0
## 25 HPV18, HPV16, HPV4, HPV17 0 0
## 26 HPV18, HPV16, HPV4, HPV17 0 0
## 27 HPV18, HPV16, HPV4, HPV17 0 0
## 28 HPV18, HPV16, HPV4, HPV17 0 0
## 29 HPV18, HPV16, HPV4, HPV17 0 0
## 30 HPV18, HPV16, HPV4, HPV17 0 0
## 31 HPV18, HPV16, HPV4, HPV17 0 0
## 32 HPV18, HPV16, HPV4, HPV17 0 0
## 33 HPV18, HPV16, HPV4, HPV17 0 0
## 34 HPV18, HPV16, HPV4, HPV17 0 0
## 35 HPV18, HPV16, HPV4, HPV17 0 0
## 36 HPV18, HPV16, HPV4, HPV17 0 0
## 37 HPV18, HPV16, HPV4, HPV17 0 0
## 38 HPV18, HPV16, HPV4, HPV17 0 0
## 39 HPV18, HPV16, HPV4, HPV17 0 0
## 40 HPV18, HPV16, HPV4, HPV17 0 0
## 41 HPV18, HPV16, HPV4, HPV17 0 0
## 42 HPV18, HPV16, HPV4, HPV17 0 0
## 43 HPV18, HPV16, HPV4, HPV17 0 0
## 44 HPV18, HPV16, HPV4, HPV17 0 0
## 45 HPV18, HPV16, HPV4, HPV17 0 0
## 46 HPV18, HPV16, HPV4, HPV17 0 0
## 47 HPV18, HPV16, HPV4, HPV17 0 0
## 48 HPV18, HPV16, HPV4, HPV17 0 0
## 49 HPV18, HPV16, HPV4, HPV17 0 0
## 50 HPV18, HPV16, HPV4, HPV17 0 0
## 51 HPV18, HPV16, HPV4, HPV17 0 0
## 52 HPV18, HPV16, HPV4, HPV17 0 0
## 53 HPV18, HPV16, HPV4, HPV17 0 0
## 54 HPV18, HPV16, HPV4, HPV17 0 0
## 55 HPV18, HPV16, HPV4, HPV17 0 0
## 56 HPV18, HPV16, HPV4, HPV17 0 0
## 57 HPV18, HPV16, HPV4, HPV17 0 0
## 58 HPV18, HPV16, HPV4, HPV17 0 0
## 59 HPV18, HPV16, HPV4, HPV17 0 0
## 60 HPV18, HPV16, HPV4, HPV17 0 0
## 61 HPV18, HPV16, HPV4, HPV17 0 0
## 62 HPV18, HPV16, HPV4, HPV17 0 0
## 63 HPV18, HPV16, HPV4, HPV17 0 0
## 64 HPV18, HPV16, HPV4, HPV17 0 0
## 65 HPV18, HPV16, HPV4, HPV17 0 0
## 66 HPV18, HPV16, HPV4, HPV17 0 0
## 67 HPV18, HPV16, HPV4, HPV17 0 0
## 68 HPV18, HPV16, HPV4, HPV17 0 0
## 69 HPV18, HPV16, HPV4, HPV17 0 0
## 70 HPV18, HPV16, HPV4, HPV17 0 0
## 71 HPV18, HPV16, HPV4, HPV17 0 0
## 72 HPV18, HPV16, HPV4, HPV17 0 0
## 73 HPV18, HPV16, HPV4, HPV17 0 0
## 74 HPV18, HPV16, HPV4, HPV17 0 0
## 75 HPV18, HPV16, HPV4, HPV17 0 0
## 76 HPV18, HPV16, HPV4, HPV17 0 0
## 77 HPV18, HPV16, HPV4, HPV17 0 0
## 78 HPV18, HPV16, HPV4, HPV17 0 0
## 79 HPV18, HPV16, HPV4, HPV17 0 0
## 80 HPV18, HPV16, HPV4, HPV17 0 0
## 81 HPV18, HPV16, HPV4, HPV17 0 0
## 82 HPV18, HPV16, HPV4, HPV17 0 0
## 83 HPV18, HPV16, HPV4, HPV17 0 0
## 84 HPV18, HPV16, HPV4, HPV17 0 0
## 85 HPV18, HPV16, HPV4, HPV17 0 0
## 86 HPV18, HPV16, HPV4, HPV17 0 0
## 87 HPV18, HPV16, HPV4, HPV17 0 0
## 88 HPV18, HPV16, HPV4, HPV17 0 0
## 89 HPV18, HPV16, HPV4, HPV17 0 0
## 90 HPV18, HPV16, HPV4, HPV17 0 0
## 91 HPV18, HPV16, HPV4, HPV17 0 0
## 92 HPV18, HPV16, HPV4, HPV17 0 0
## 93 HPV18, HPV16, HPV4, HPV17 0 0
## 94 HPV18, HPV16, HPV4, HPV17 0 0
## 95 HPV18, HPV16, HPV4, HPV17 0 0
## 96 HPV18, HPV16, HPV4, HPV17 0 0
## 97 HPV18, HPV16, HPV4, HPV17 0 0
## 98 HPV18, HPV16, HPV4, HPV17 0 0
## 99 HPV18, HPV16, HPV4, HPV17 0 0
## 100 HPV18, HPV16, HPV4, HPV17 0 0
##
## [[6]]
## forward_primer reverse_primer score coverage products
## 1 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGTT 0 0.2 0
## 2 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGT 0 0.2 0
## 3 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 4 GTTTGACCCCACTACACAGCG ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 5 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCT 0 0.2 0
## 6 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 7 GTTTGACCCCACTACACAGCG ACTAACACCAACGCCTAAAGGTTG 0 0.2 0
## 8 GTTTGACCCCACTACACAGCG CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 9 GTTTGACCCCACTACACAGCG CCACTAACRCCAACRCCTAAAGG 0 0.2 0
## 10 GTTTGACCCCACTACACAGCG GGATGCCCACTAACACCAACG 0 0.2 0
## 11 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAAG 0 0.2 0
## 12 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCTC 0 0.2 0
## 13 GTTTGACCCCACTACACAGCG GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 14 GTTTGACCCCACTACACAGCG TGCCCACTAACACCAACGC 0 0.2 0
## 15 GTTTGACCCCACTACACAGCG TGACCCCTGCCTACCTCC 0 0.2 0
## 16 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 17 GTTTGACCCCACTACACAGCG CAACGCCTAAAGGTTGACCCC 0 0.2 0
## 18 GTTTGACCCCACTACACAGCG CCAACGCCTAAAGGTTGACCC 0 0.2 0
## 19 GTTTGACCCCACTACACAGCG AGGTTGACCCCTGCCTACC 0 0.2 0
## 20 GTTTGACCCCACTACACAGCG ACCAACGCCTAAAGGTTGACC 0 0.2 0
## 21 GTTTGACCCCACTACACAGCG GCAATGGATGCCCACTAACACC 0 0.2 0
## 22 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 23 GTTTGACCCCACTACACAGCG ACACCAACGCCTAAAGGTTGAC 0 0.2 0
## 24 GTTTGACCCCACTACACAGCG AGCAATGGATGCCCACTAACAC 0 0.2 0
## 25 GTTTGACCCCACTACACAGCG TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 26 GTTTGACCCCACTACACAGCG ACCCCTGCCTACCTCCAAC 0 0.2 0
## 27 GTTTGACCCCACTACACAGCG ATGGATGCCCACTAACACCAAC 0 0.2 0
## 28 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 29 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTA 0 0.2 0
## 30 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 31 GTTTGACCCCACTACACAGCG CTAACACCAACGCCTAAAGGTTGA 0 0.2 0
## 32 GTTTGACCCCACTACACAGCG CACCYCTRCCTACCTCCA 0 0.2 0
## 33 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCA 0 0.2 0
## 34 GTTTGACCCCACTACACAGCG GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 35 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTAA 0 0.2 0
## 36 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 37 GTTTGACCCCACTACACAGCG GACCCCTGCCTACCTCCAA 0 0.2 0
## 38 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCAA 0 0.2 0
## 39 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAA 0 0.2 0
## 40 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 41 TGACCCCACTACACAGCGTT ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 42 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCT 0 0.2 0
## 43 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 44 TGACCCCACTACACAGCGTT CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 45 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCTC 0 0.2 0
## 46 TGACCCCACTACACAGCGTT GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 47 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 48 TGACCCCACTACACAGCGTT AGGTTGACCCCTGCCTACC 0 0.2 0
## 49 TGACCCCACTACACAGCGTT GCAATGGATGCCCACTAACACC 0 0.2 0
## 50 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 51 TGACCCCACTACACAGCGTT AGCAATGGATGCCCACTAACAC 0 0.2 0
## 52 TGACCCCACTACACAGCGTT TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 53 TGACCCCACTACACAGCGTT ATGGATGCCCACTAACACCAAC 0 0.2 0
## 54 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 55 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 56 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCA 0 0.2 0
## 57 TGACCCCACTACACAGCGTT GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 58 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 59 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCAA 0 0.2 0
## 60 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGT 0 0.2 0
## 61 TCCTTGCTGTGGGACATCCAT CACGCCCATACTAAACGCTGT 0 0.2 0
## 62 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGT 0 0.2 0
## 63 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGT 0 0.2 0
## 64 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAGT 0 0.2 0
## 65 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCT 0 0.2 0
## 66 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCT 0 0.2 0
## 67 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACT 0 0.2 0
## 68 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGAT 0 0.2 0
## 69 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGAAT 0 0.2 0
## 70 TCCTTGCTGTGGGACATCCAT ACGCCCATACTAAACGCTGTG 0 0.2 0
## 71 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGTG 0 0.2 0
## 72 TCCTTGCTGTGGGACATCCAT GCCCATACTAAACGCTGTGTAGTG 0 0.2 0
## 73 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCTG 0 0.2 0
## 74 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCTG 0 0.2 0
## 75 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGATG 0 0.2 0
## 76 TCCTTGCTGTGGGACATCCAT CATACTAAACGCTGTGTAGTGGGG 0 0.2 0
## 77 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGG 0 0.2 0
## 78 TCCTTGCTGTGGGACATCCAT CCTCCAACCCTGTGCACG 0 0.2 0
## 79 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAG 0 0.2 0
## 80 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGAG 0 0.2 0
## 81 TCCTTGCTGTGGGACATCCAT GTGGGGTCAAACAGAGATGAATCAG 0 0.2 0
## 82 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAG 0 0.2 0
## 83 TCCTTGCTGTGGGACATCCAT CTAAACGCTGTGTAGTGGGGTC 0 0.2 0
## 84 TCCTTGCTGTGGGACATCCAT GCCTACCTCCAACCCTGTGC 0 0.2 0
## 85 TCCTTGCTGTGGGACATCCAT TCCAACCCTGTGCACGC 0 0.2 0
## 86 TCCTTGCTGTGGGACATCCAT CCAACCCTGTGCACGCC 0 0.2 0
## 87 TCCTTGCTGTGGGACATCCAT CCCTGCCTACCTCCAACCC 0 0.2 0
## 88 TCCTTGCTGTGGGACATCCAT CCCCTGCCTACCTCCAACC 0 0.2 0
## 89 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATAC 0 0.2 0
## 90 TCCTTGCTGTGGGACATCCAT CCTACCTCCAACCCTGTGCAC 0 0.2 0
## 91 TCCTTGCTGTGGGACATCCAT ACCCCTGCCTACCTCCAAC 0 0.2 0
## 92 TCCTTGCTGTGGGACATCCAT CCTGTGCACGCCCATACTAAAC 0 0.2 0
## 93 TCCTTGCTGTGGGACATCCAT CGCTGTGTAGTGGGGTCAAAC 0 0.2 0
## 94 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTA 0 0.2 0
## 95 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGTA 0 0.2 0
## 96 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACTA 0 0.2 0
## 97 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATA 0 0.2 0
## 98 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGA 0 0.2 0
## 99 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGA 0 0.2 0
## 100 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGA 0 0.2 0
## similar_signatures missing_signatures enzyme digest_score fragments
## 1 HPV18, HPV16, HPV4, HPV17 0 0
## 2 HPV18, HPV16, HPV4, HPV17 0 0
## 3 HPV18, HPV16, HPV4, HPV17 0 0
## 4 HPV18, HPV16, HPV4, HPV17 0 0
## 5 HPV18, HPV16, HPV4, HPV17 0 0
## 6 HPV18, HPV16, HPV4, HPV17 0 0
## 7 HPV18, HPV16, HPV4, HPV17 0 0
## 8 HPV18, HPV16, HPV4, HPV17 0 0
## 9 HPV18, HPV16, HPV4, HPV17 0 0
## 10 HPV18, HPV16, HPV4, HPV17 0 0
## 11 HPV18, HPV16, HPV4, HPV17 0 0
## 12 HPV18, HPV16, HPV4, HPV17 0 0
## 13 HPV18, HPV16, HPV4, HPV17 0 0
## 14 HPV18, HPV16, HPV4, HPV17 0 0
## 15 HPV18, HPV16, HPV4, HPV17 0 0
## 16 HPV18, HPV16, HPV4, HPV17 0 0
## 17 HPV18, HPV16, HPV4, HPV17 0 0
## 18 HPV18, HPV16, HPV4, HPV17 0 0
## 19 HPV18, HPV16, HPV4, HPV17 0 0
## 20 HPV18, HPV16, HPV4, HPV17 0 0
## 21 HPV18, HPV16, HPV4, HPV17 0 0
## 22 HPV18, HPV16, HPV4, HPV17 0 0
## 23 HPV18, HPV16, HPV4, HPV17 0 0
## 24 HPV18, HPV16, HPV4, HPV17 0 0
## 25 HPV18, HPV16, HPV4, HPV17 0 0
## 26 HPV18, HPV16, HPV4, HPV17 0 0
## 27 HPV18, HPV16, HPV4, HPV17 0 0
## 28 HPV18, HPV16, HPV4, HPV17 0 0
## 29 HPV18, HPV16, HPV4, HPV17 0 0
## 30 HPV18, HPV16, HPV4, HPV17 0 0
## 31 HPV18, HPV16, HPV4, HPV17 0 0
## 32 HPV18, HPV16, HPV4, HPV17 0 0
## 33 HPV18, HPV16, HPV4, HPV17 0 0
## 34 HPV18, HPV16, HPV4, HPV17 0 0
## 35 HPV18, HPV16, HPV4, HPV17 0 0
## 36 HPV18, HPV16, HPV4, HPV17 0 0
## 37 HPV18, HPV16, HPV4, HPV17 0 0
## 38 HPV18, HPV16, HPV4, HPV17 0 0
## 39 HPV18, HPV16, HPV4, HPV17 0 0
## 40 HPV18, HPV16, HPV4, HPV17 0 0
## 41 HPV18, HPV16, HPV4, HPV17 0 0
## 42 HPV18, HPV16, HPV4, HPV17 0 0
## 43 HPV18, HPV16, HPV4, HPV17 0 0
## 44 HPV18, HPV16, HPV4, HPV17 0 0
## 45 HPV18, HPV16, HPV4, HPV17 0 0
## 46 HPV18, HPV16, HPV4, HPV17 0 0
## 47 HPV18, HPV16, HPV4, HPV17 0 0
## 48 HPV18, HPV16, HPV4, HPV17 0 0
## 49 HPV18, HPV16, HPV4, HPV17 0 0
## 50 HPV18, HPV16, HPV4, HPV17 0 0
## 51 HPV18, HPV16, HPV4, HPV17 0 0
## 52 HPV18, HPV16, HPV4, HPV17 0 0
## 53 HPV18, HPV16, HPV4, HPV17 0 0
## 54 HPV18, HPV16, HPV4, HPV17 0 0
## 55 HPV18, HPV16, HPV4, HPV17 0 0
## 56 HPV18, HPV16, HPV4, HPV17 0 0
## 57 HPV18, HPV16, HPV4, HPV17 0 0
## 58 HPV18, HPV16, HPV4, HPV17 0 0
## 59 HPV18, HPV16, HPV4, HPV17 0 0
## 60 HPV18, HPV16, HPV4, HPV17 0 0
## 61 HPV18, HPV16, HPV4, HPV17 0 0
## 62 HPV18, HPV16, HPV4, HPV17 0 0
## 63 HPV18, HPV16, HPV4, HPV17 0 0
## 64 HPV18, HPV16, HPV4, HPV17 0 0
## 65 HPV18, HPV16, HPV4, HPV17 0 0
## 66 HPV18, HPV16, HPV4, HPV17 0 0
## 67 HPV18, HPV16, HPV4, HPV17 0 0
## 68 HPV18, HPV16, HPV4, HPV17 0 0
## 69 HPV18, HPV16, HPV4, HPV17 0 0
## 70 HPV18, HPV16, HPV4, HPV17 0 0
## 71 HPV18, HPV16, HPV4, HPV17 0 0
## 72 HPV18, HPV16, HPV4, HPV17 0 0
## 73 HPV18, HPV16, HPV4, HPV17 0 0
## 74 HPV18, HPV16, HPV4, HPV17 0 0
## 75 HPV18, HPV16, HPV4, HPV17 0 0
## 76 HPV18, HPV16, HPV4, HPV17 0 0
## 77 HPV18, HPV16, HPV4, HPV17 0 0
## 78 HPV18, HPV16, HPV4, HPV17 0 0
## 79 HPV18, HPV16, HPV4, HPV17 0 0
## 80 HPV18, HPV16, HPV4, HPV17 0 0
## 81 HPV18, HPV16, HPV4, HPV17 0 0
## 82 HPV18, HPV16, HPV4, HPV17 0 0
## 83 HPV18, HPV16, HPV4, HPV17 0 0
## 84 HPV18, HPV16, HPV4, HPV17 0 0
## 85 HPV18, HPV16, HPV4, HPV17 0 0
## 86 HPV18, HPV16, HPV4, HPV17 0 0
## 87 HPV18, HPV16, HPV4, HPV17 0 0
## 88 HPV18, HPV16, HPV4, HPV17 0 0
## 89 HPV18, HPV16, HPV4, HPV17 0 0
## 90 HPV18, HPV16, HPV4, HPV17 0 0
## 91 HPV18, HPV16, HPV4, HPV17 0 0
## 92 HPV18, HPV16, HPV4, HPV17 0 0
## 93 HPV18, HPV16, HPV4, HPV17 0 0
## 94 HPV18, HPV16, HPV4, HPV17 0 0
## 95 HPV18, HPV16, HPV4, HPV17 0 0
## 96 HPV18, HPV16, HPV4, HPV17 0 0
## 97 HPV18, HPV16, HPV4, HPV17 0 0
## 98 HPV18, HPV16, HPV4, HPV17 0 0
## 99 HPV18, HPV16, HPV4, HPV17 0 0
## 100 HPV18, HPV16, HPV4, HPV17 0 0
##
## [[7]]
## forward_primer reverse_primer score coverage products
## 1 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 2 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 3 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGTT 0 0.2 0
## 4 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGT 0 0.2 0
## 5 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 6 GTTTGACCCCACTACACAGCG ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 7 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCT 0 0.2 0
## 8 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 9 GTTTGACCCCACTACACAGCG ACTAACACCAACGCCTAAAGGTTG 0 0.2 0
## 10 GTTTGACCCCACTACACAGCG CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 11 GTTTGACCCCACTACACAGCG CCACTAACRCCAACRCCTAAAGG 0 0.2 0
## 12 GTTTGACCCCACTACACAGCG GGATGCCCACTAACACCAACG 0 0.2 0
## 13 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAAG 0 0.2 0
## 14 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCTC 0 0.2 0
## 15 GTTTGACCCCACTACACAGCG GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 16 GTTTGACCCCACTACACAGCG TGCCCACTAACACCAACGC 0 0.2 0
## 17 GTTTGACCCCACTACACAGCG TGACCCCTGCCTACCTCC 0 0.2 0
## 18 GTTTGACCCCACTACACAGCG CAACGCCTAAAGGTTGACCCC 0 0.2 0
## 19 GTTTGACCCCACTACACAGCG CCAACGCCTAAAGGTTGACCC 0 0.2 0
## 20 GTTTGACCCCACTACACAGCG AGGTTGACCCCTGCCTACC 0 0.2 0
## 21 GTTTGACCCCACTACACAGCG ACCAACGCCTAAAGGTTGACC 0 0.2 0
## 22 GTTTGACCCCACTACACAGCG GCAATGGATGCCCACTAACACC 0 0.2 0
## 23 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 24 GTTTGACCCCACTACACAGCG ACACCAACGCCTAAAGGTTGAC 0 0.2 0
## 25 GTTTGACCCCACTACACAGCG AGCAATGGATGCCCACTAACAC 0 0.2 0
## 26 GTTTGACCCCACTACACAGCG TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 27 GTTTGACCCCACTACACAGCG ACCCCTGCCTACCTCCAAC 0 0.2 0
## 28 GTTTGACCCCACTACACAGCG ATGGATGCCCACTAACACCAAC 0 0.2 0
## 29 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 30 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTA 0 0.2 0
## 31 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 32 GTTTGACCCCACTACACAGCG CTAACACCAACGCCTAAAGGTTGA 0 0.2 0
## 33 GTTTGACCCCACTACACAGCG CACCYCTRCCTACCTCCA 0 0.2 0
## 34 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCA 0 0.2 0
## 35 GTTTGACCCCACTACACAGCG GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 36 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTAA 0 0.2 0
## 37 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 38 GTTTGACCCCACTACACAGCG GACCCCTGCCTACCTCCAA 0 0.2 0
## 39 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCAA 0 0.2 0
## 40 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAA 0 0.2 0
## 41 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 42 TGACCCCACTACACAGCGTT ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 43 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCT 0 0.2 0
## 44 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 45 TGACCCCACTACACAGCGTT CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 46 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCTC 0 0.2 0
## 47 TGACCCCACTACACAGCGTT GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 48 TGACCCCACTACACAGCGTT AGGTTGACCCCTGCCTACC 0 0.2 0
## 49 TGACCCCACTACACAGCGTT GCAATGGATGCCCACTAACACC 0 0.2 0
## 50 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 51 TGACCCCACTACACAGCGTT AGCAATGGATGCCCACTAACAC 0 0.2 0
## 52 TGACCCCACTACACAGCGTT TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 53 TGACCCCACTACACAGCGTT ATGGATGCCCACTAACACCAAC 0 0.2 0
## 54 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 55 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 56 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCA 0 0.2 0
## 57 TGACCCCACTACACAGCGTT GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 58 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 59 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCAA 0 0.2 0
## 60 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGT 0 0.2 0
## 61 TCCTTGCTGTGGGACATCCAT CACGCCCATACTAAACGCTGT 0 0.2 0
## 62 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGT 0 0.2 0
## 63 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGT 0 0.2 0
## 64 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAGT 0 0.2 0
## 65 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCT 0 0.2 0
## 66 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCT 0 0.2 0
## 67 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACT 0 0.2 0
## 68 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGAT 0 0.2 0
## 69 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGAAT 0 0.2 0
## 70 TCCTTGCTGTGGGACATCCAT ACGCCCATACTAAACGCTGTG 0 0.2 0
## 71 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGTG 0 0.2 0
## 72 TCCTTGCTGTGGGACATCCAT GCCCATACTAAACGCTGTGTAGTG 0 0.2 0
## 73 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCTG 0 0.2 0
## 74 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCTG 0 0.2 0
## 75 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGATG 0 0.2 0
## 76 TCCTTGCTGTGGGACATCCAT CATACTAAACGCTGTGTAGTGGGG 0 0.2 0
## 77 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGG 0 0.2 0
## 78 TCCTTGCTGTGGGACATCCAT CCTCCAACCCTGTGCACG 0 0.2 0
## 79 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAG 0 0.2 0
## 80 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGAG 0 0.2 0
## 81 TCCTTGCTGTGGGACATCCAT GTGGGGTCAAACAGAGATGAATCAG 0 0.2 0
## 82 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAG 0 0.2 0
## 83 TCCTTGCTGTGGGACATCCAT CTAAACGCTGTGTAGTGGGGTC 0 0.2 0
## 84 TCCTTGCTGTGGGACATCCAT GCCTACCTCCAACCCTGTGC 0 0.2 0
## 85 TCCTTGCTGTGGGACATCCAT TCCAACCCTGTGCACGC 0 0.2 0
## 86 TCCTTGCTGTGGGACATCCAT CCAACCCTGTGCACGCC 0 0.2 0
## 87 TCCTTGCTGTGGGACATCCAT CCCTGCCTACCTCCAACCC 0 0.2 0
## 88 TCCTTGCTGTGGGACATCCAT CCCCTGCCTACCTCCAACC 0 0.2 0
## 89 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATAC 0 0.2 0
## 90 TCCTTGCTGTGGGACATCCAT CCTACCTCCAACCCTGTGCAC 0 0.2 0
## 91 TCCTTGCTGTGGGACATCCAT ACCCCTGCCTACCTCCAAC 0 0.2 0
## 92 TCCTTGCTGTGGGACATCCAT CCTGTGCACGCCCATACTAAAC 0 0.2 0
## 93 TCCTTGCTGTGGGACATCCAT CGCTGTGTAGTGGGGTCAAAC 0 0.2 0
## 94 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTA 0 0.2 0
## 95 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGTA 0 0.2 0
## 96 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACTA 0 0.2 0
## 97 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATA 0 0.2 0
## 98 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGA 0 0.2 0
## 99 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGA 0 0.2 0
## 100 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGA 0 0.2 0
## similar_signatures missing_signatures enzyme digest_score fragments
## 1 HPV18, HPV16, HPV4, HPV17 Acc65I 0 2
## 2 HPV18, HPV16, HPV4, HPV17 Acc65I 0 2
## 3 HPV18, HPV16, HPV4, HPV17 0 0
## 4 HPV18, HPV16, HPV4, HPV17 0 0
## 5 HPV18, HPV16, HPV4, HPV17 0 0
## 6 HPV18, HPV16, HPV4, HPV17 0 0
## 7 HPV18, HPV16, HPV4, HPV17 0 0
## 8 HPV18, HPV16, HPV4, HPV17 0 0
## 9 HPV18, HPV16, HPV4, HPV17 0 0
## 10 HPV18, HPV16, HPV4, HPV17 0 0
## 11 HPV18, HPV16, HPV4, HPV17 0 0
## 12 HPV18, HPV16, HPV4, HPV17 0 0
## 13 HPV18, HPV16, HPV4, HPV17 0 0
## 14 HPV18, HPV16, HPV4, HPV17 0 0
## 15 HPV18, HPV16, HPV4, HPV17 0 0
## 16 HPV18, HPV16, HPV4, HPV17 0 0
## 17 HPV18, HPV16, HPV4, HPV17 0 0
## 18 HPV18, HPV16, HPV4, HPV17 0 0
## 19 HPV18, HPV16, HPV4, HPV17 0 0
## 20 HPV18, HPV16, HPV4, HPV17 0 0
## 21 HPV18, HPV16, HPV4, HPV17 0 0
## 22 HPV18, HPV16, HPV4, HPV17 0 0
## 23 HPV18, HPV16, HPV4, HPV17 0 0
## 24 HPV18, HPV16, HPV4, HPV17 0 0
## 25 HPV18, HPV16, HPV4, HPV17 0 0
## 26 HPV18, HPV16, HPV4, HPV17 0 0
## 27 HPV18, HPV16, HPV4, HPV17 0 0
## 28 HPV18, HPV16, HPV4, HPV17 0 0
## 29 HPV18, HPV16, HPV4, HPV17 0 0
## 30 HPV18, HPV16, HPV4, HPV17 0 0
## 31 HPV18, HPV16, HPV4, HPV17 0 0
## 32 HPV18, HPV16, HPV4, HPV17 0 0
## 33 HPV18, HPV16, HPV4, HPV17 0 0
## 34 HPV18, HPV16, HPV4, HPV17 0 0
## 35 HPV18, HPV16, HPV4, HPV17 0 0
## 36 HPV18, HPV16, HPV4, HPV17 0 0
## 37 HPV18, HPV16, HPV4, HPV17 0 0
## 38 HPV18, HPV16, HPV4, HPV17 0 0
## 39 HPV18, HPV16, HPV4, HPV17 0 0
## 40 HPV18, HPV16, HPV4, HPV17 0 0
## 41 HPV18, HPV16, HPV4, HPV17 0 0
## 42 HPV18, HPV16, HPV4, HPV17 0 0
## 43 HPV18, HPV16, HPV4, HPV17 0 0
## 44 HPV18, HPV16, HPV4, HPV17 0 0
## 45 HPV18, HPV16, HPV4, HPV17 0 0
## 46 HPV18, HPV16, HPV4, HPV17 0 0
## 47 HPV18, HPV16, HPV4, HPV17 0 0
## 48 HPV18, HPV16, HPV4, HPV17 0 0
## 49 HPV18, HPV16, HPV4, HPV17 0 0
## 50 HPV18, HPV16, HPV4, HPV17 0 0
## 51 HPV18, HPV16, HPV4, HPV17 0 0
## 52 HPV18, HPV16, HPV4, HPV17 0 0
## 53 HPV18, HPV16, HPV4, HPV17 0 0
## 54 HPV18, HPV16, HPV4, HPV17 0 0
## 55 HPV18, HPV16, HPV4, HPV17 0 0
## 56 HPV18, HPV16, HPV4, HPV17 0 0
## 57 HPV18, HPV16, HPV4, HPV17 0 0
## 58 HPV18, HPV16, HPV4, HPV17 0 0
## 59 HPV18, HPV16, HPV4, HPV17 0 0
## 60 HPV18, HPV16, HPV4, HPV17 0 0
## 61 HPV18, HPV16, HPV4, HPV17 0 0
## 62 HPV18, HPV16, HPV4, HPV17 0 0
## 63 HPV18, HPV16, HPV4, HPV17 0 0
## 64 HPV18, HPV16, HPV4, HPV17 0 0
## 65 HPV18, HPV16, HPV4, HPV17 0 0
## 66 HPV18, HPV16, HPV4, HPV17 0 0
## 67 HPV18, HPV16, HPV4, HPV17 0 0
## 68 HPV18, HPV16, HPV4, HPV17 0 0
## 69 HPV18, HPV16, HPV4, HPV17 0 0
## 70 HPV18, HPV16, HPV4, HPV17 0 0
## 71 HPV18, HPV16, HPV4, HPV17 0 0
## 72 HPV18, HPV16, HPV4, HPV17 0 0
## 73 HPV18, HPV16, HPV4, HPV17 0 0
## 74 HPV18, HPV16, HPV4, HPV17 0 0
## 75 HPV18, HPV16, HPV4, HPV17 0 0
## 76 HPV18, HPV16, HPV4, HPV17 0 0
## 77 HPV18, HPV16, HPV4, HPV17 0 0
## 78 HPV18, HPV16, HPV4, HPV17 0 0
## 79 HPV18, HPV16, HPV4, HPV17 0 0
## 80 HPV18, HPV16, HPV4, HPV17 0 0
## 81 HPV18, HPV16, HPV4, HPV17 0 0
## 82 HPV18, HPV16, HPV4, HPV17 0 0
## 83 HPV18, HPV16, HPV4, HPV17 0 0
## 84 HPV18, HPV16, HPV4, HPV17 0 0
## 85 HPV18, HPV16, HPV4, HPV17 0 0
## 86 HPV18, HPV16, HPV4, HPV17 0 0
## 87 HPV18, HPV16, HPV4, HPV17 0 0
## 88 HPV18, HPV16, HPV4, HPV17 0 0
## 89 HPV18, HPV16, HPV4, HPV17 0 0
## 90 HPV18, HPV16, HPV4, HPV17 0 0
## 91 HPV18, HPV16, HPV4, HPV17 0 0
## 92 HPV18, HPV16, HPV4, HPV17 0 0
## 93 HPV18, HPV16, HPV4, HPV17 0 0
## 94 HPV18, HPV16, HPV4, HPV17 0 0
## 95 HPV18, HPV16, HPV4, HPV17 0 0
## 96 HPV18, HPV16, HPV4, HPV17 0 0
## 97 HPV18, HPV16, HPV4, HPV17 0 0
## 98 HPV18, HPV16, HPV4, HPV17 0 0
## 99 HPV18, HPV16, HPV4, HPV17 0 0
## 100 HPV18, HPV16, HPV4, HPV17 0 0
##
## [[8]]
## forward_primer reverse_primer score coverage products
## 1 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGTT 0 0.2 0
## 2 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGT 0 0.2 0
## 3 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 4 GTTTGACCCCACTACACAGCG ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 5 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCT 0 0.2 0
## 6 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 7 GTTTGACCCCACTACACAGCG ACTAACACCAACGCCTAAAGGTTG 0 0.2 0
## 8 GTTTGACCCCACTACACAGCG CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 9 GTTTGACCCCACTACACAGCG CCACTAACRCCAACRCCTAAAGG 0 0.2 0
## 10 GTTTGACCCCACTACACAGCG GGATGCCCACTAACACCAACG 0 0.2 0
## 11 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAAG 0 0.2 0
## 12 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCTC 0 0.2 0
## 13 GTTTGACCCCACTACACAGCG GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 14 GTTTGACCCCACTACACAGCG TGCCCACTAACACCAACGC 0 0.2 0
## 15 GTTTGACCCCACTACACAGCG TGACCCCTGCCTACCTCC 0 0.2 0
## 16 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 17 GTTTGACCCCACTACACAGCG CAACGCCTAAAGGTTGACCCC 0 0.2 0
## 18 GTTTGACCCCACTACACAGCG CCAACGCCTAAAGGTTGACCC 0 0.2 0
## 19 GTTTGACCCCACTACACAGCG AGGTTGACCCCTGCCTACC 0 0.2 0
## 20 GTTTGACCCCACTACACAGCG ACCAACGCCTAAAGGTTGACC 0 0.2 0
## 21 GTTTGACCCCACTACACAGCG GCAATGGATGCCCACTAACACC 0 0.2 0
## 22 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 23 GTTTGACCCCACTACACAGCG ACACCAACGCCTAAAGGTTGAC 0 0.2 0
## 24 GTTTGACCCCACTACACAGCG AGCAATGGATGCCCACTAACAC 0 0.2 0
## 25 GTTTGACCCCACTACACAGCG TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 26 GTTTGACCCCACTACACAGCG ACCCCTGCCTACCTCCAAC 0 0.2 0
## 27 GTTTGACCCCACTACACAGCG ATGGATGCCCACTAACACCAAC 0 0.2 0
## 28 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 29 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTA 0 0.2 0
## 30 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 31 GTTTGACCCCACTACACAGCG CTAACACCAACGCCTAAAGGTTGA 0 0.2 0
## 32 GTTTGACCCCACTACACAGCG CACCYCTRCCTACCTCCA 0 0.2 0
## 33 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCA 0 0.2 0
## 34 GTTTGACCCCACTACACAGCG GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 35 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTAA 0 0.2 0
## 36 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 37 GTTTGACCCCACTACACAGCG GACCCCTGCCTACCTCCAA 0 0.2 0
## 38 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCAA 0 0.2 0
## 39 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAA 0 0.2 0
## 40 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 41 TGACCCCACTACACAGCGTT ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 42 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCT 0 0.2 0
## 43 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 44 TGACCCCACTACACAGCGTT CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 45 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCTC 0 0.2 0
## 46 TGACCCCACTACACAGCGTT GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 47 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 48 TGACCCCACTACACAGCGTT AGGTTGACCCCTGCCTACC 0 0.2 0
## 49 TGACCCCACTACACAGCGTT GCAATGGATGCCCACTAACACC 0 0.2 0
## 50 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 51 TGACCCCACTACACAGCGTT AGCAATGGATGCCCACTAACAC 0 0.2 0
## 52 TGACCCCACTACACAGCGTT TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 53 TGACCCCACTACACAGCGTT ATGGATGCCCACTAACACCAAC 0 0.2 0
## 54 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 55 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 56 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCA 0 0.2 0
## 57 TGACCCCACTACACAGCGTT GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 58 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 59 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCAA 0 0.2 0
## 60 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGT 0 0.2 0
## 61 TCCTTGCTGTGGGACATCCAT CACGCCCATACTAAACGCTGT 0 0.2 0
## 62 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGT 0 0.2 0
## 63 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGT 0 0.2 0
## 64 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAGT 0 0.2 0
## 65 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCT 0 0.2 0
## 66 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCT 0 0.2 0
## 67 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACT 0 0.2 0
## 68 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGAT 0 0.2 0
## 69 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGAAT 0 0.2 0
## 70 TCCTTGCTGTGGGACATCCAT ACGCCCATACTAAACGCTGTG 0 0.2 0
## 71 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGTG 0 0.2 0
## 72 TCCTTGCTGTGGGACATCCAT GCCCATACTAAACGCTGTGTAGTG 0 0.2 0
## 73 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCTG 0 0.2 0
## 74 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCTG 0 0.2 0
## 75 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGATG 0 0.2 0
## 76 TCCTTGCTGTGGGACATCCAT CATACTAAACGCTGTGTAGTGGGG 0 0.2 0
## 77 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGG 0 0.2 0
## 78 TCCTTGCTGTGGGACATCCAT CCTCCAACCCTGTGCACG 0 0.2 0
## 79 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAG 0 0.2 0
## 80 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGAG 0 0.2 0
## 81 TCCTTGCTGTGGGACATCCAT GTGGGGTCAAACAGAGATGAATCAG 0 0.2 0
## 82 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAG 0 0.2 0
## 83 TCCTTGCTGTGGGACATCCAT CTAAACGCTGTGTAGTGGGGTC 0 0.2 0
## 84 TCCTTGCTGTGGGACATCCAT GCCTACCTCCAACCCTGTGC 0 0.2 0
## 85 TCCTTGCTGTGGGACATCCAT TCCAACCCTGTGCACGC 0 0.2 0
## 86 TCCTTGCTGTGGGACATCCAT CCAACCCTGTGCACGCC 0 0.2 0
## 87 TCCTTGCTGTGGGACATCCAT CCCTGCCTACCTCCAACCC 0 0.2 0
## 88 TCCTTGCTGTGGGACATCCAT CCCCTGCCTACCTCCAACC 0 0.2 0
## 89 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATAC 0 0.2 0
## 90 TCCTTGCTGTGGGACATCCAT CCTACCTCCAACCCTGTGCAC 0 0.2 0
## 91 TCCTTGCTGTGGGACATCCAT ACCCCTGCCTACCTCCAAC 0 0.2 0
## 92 TCCTTGCTGTGGGACATCCAT CCTGTGCACGCCCATACTAAAC 0 0.2 0
## 93 TCCTTGCTGTGGGACATCCAT CGCTGTGTAGTGGGGTCAAAC 0 0.2 0
## 94 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTA 0 0.2 0
## 95 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGTA 0 0.2 0
## 96 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACTA 0 0.2 0
## 97 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATA 0 0.2 0
## 98 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGA 0 0.2 0
## 99 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGA 0 0.2 0
## 100 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGA 0 0.2 0
## similar_signatures missing_signatures enzyme digest_score fragments
## 1 HPV18, HPV16, HPV4, HPV17 0 0
## 2 HPV18, HPV16, HPV4, HPV17 0 0
## 3 HPV18, HPV16, HPV4, HPV17 0 0
## 4 HPV18, HPV16, HPV4, HPV17 0 0
## 5 HPV18, HPV16, HPV4, HPV17 0 0
## 6 HPV18, HPV16, HPV4, HPV17 0 0
## 7 HPV18, HPV16, HPV4, HPV17 0 0
## 8 HPV18, HPV16, HPV4, HPV17 0 0
## 9 HPV18, HPV16, HPV4, HPV17 0 0
## 10 HPV18, HPV16, HPV4, HPV17 0 0
## 11 HPV18, HPV16, HPV4, HPV17 0 0
## 12 HPV18, HPV16, HPV4, HPV17 0 0
## 13 HPV18, HPV16, HPV4, HPV17 0 0
## 14 HPV18, HPV16, HPV4, HPV17 0 0
## 15 HPV18, HPV16, HPV4, HPV17 0 0
## 16 HPV18, HPV16, HPV4, HPV17 0 0
## 17 HPV18, HPV16, HPV4, HPV17 0 0
## 18 HPV18, HPV16, HPV4, HPV17 0 0
## 19 HPV18, HPV16, HPV4, HPV17 0 0
## 20 HPV18, HPV16, HPV4, HPV17 0 0
## 21 HPV18, HPV16, HPV4, HPV17 0 0
## 22 HPV18, HPV16, HPV4, HPV17 0 0
## 23 HPV18, HPV16, HPV4, HPV17 0 0
## 24 HPV18, HPV16, HPV4, HPV17 0 0
## 25 HPV18, HPV16, HPV4, HPV17 0 0
## 26 HPV18, HPV16, HPV4, HPV17 0 0
## 27 HPV18, HPV16, HPV4, HPV17 0 0
## 28 HPV18, HPV16, HPV4, HPV17 0 0
## 29 HPV18, HPV16, HPV4, HPV17 0 0
## 30 HPV18, HPV16, HPV4, HPV17 0 0
## 31 HPV18, HPV16, HPV4, HPV17 0 0
## 32 HPV18, HPV16, HPV4, HPV17 0 0
## 33 HPV18, HPV16, HPV4, HPV17 0 0
## 34 HPV18, HPV16, HPV4, HPV17 0 0
## 35 HPV18, HPV16, HPV4, HPV17 0 0
## 36 HPV18, HPV16, HPV4, HPV17 0 0
## 37 HPV18, HPV16, HPV4, HPV17 0 0
## 38 HPV18, HPV16, HPV4, HPV17 0 0
## 39 HPV18, HPV16, HPV4, HPV17 0 0
## 40 HPV18, HPV16, HPV4, HPV17 0 0
## 41 HPV18, HPV16, HPV4, HPV17 0 0
## 42 HPV18, HPV16, HPV4, HPV17 0 0
## 43 HPV18, HPV16, HPV4, HPV17 0 0
## 44 HPV18, HPV16, HPV4, HPV17 0 0
## 45 HPV18, HPV16, HPV4, HPV17 0 0
## 46 HPV18, HPV16, HPV4, HPV17 0 0
## 47 HPV18, HPV16, HPV4, HPV17 0 0
## 48 HPV18, HPV16, HPV4, HPV17 0 0
## 49 HPV18, HPV16, HPV4, HPV17 0 0
## 50 HPV18, HPV16, HPV4, HPV17 0 0
## 51 HPV18, HPV16, HPV4, HPV17 0 0
## 52 HPV18, HPV16, HPV4, HPV17 0 0
## 53 HPV18, HPV16, HPV4, HPV17 0 0
## 54 HPV18, HPV16, HPV4, HPV17 0 0
## 55 HPV18, HPV16, HPV4, HPV17 0 0
## 56 HPV18, HPV16, HPV4, HPV17 0 0
## 57 HPV18, HPV16, HPV4, HPV17 0 0
## 58 HPV18, HPV16, HPV4, HPV17 0 0
## 59 HPV18, HPV16, HPV4, HPV17 0 0
## 60 HPV18, HPV16, HPV4, HPV17 0 0
## 61 HPV18, HPV16, HPV4, HPV17 0 0
## 62 HPV18, HPV16, HPV4, HPV17 0 0
## 63 HPV18, HPV16, HPV4, HPV17 0 0
## 64 HPV18, HPV16, HPV4, HPV17 0 0
## 65 HPV18, HPV16, HPV4, HPV17 0 0
## 66 HPV18, HPV16, HPV4, HPV17 0 0
## 67 HPV18, HPV16, HPV4, HPV17 0 0
## 68 HPV18, HPV16, HPV4, HPV17 0 0
## 69 HPV18, HPV16, HPV4, HPV17 0 0
## 70 HPV18, HPV16, HPV4, HPV17 0 0
## 71 HPV18, HPV16, HPV4, HPV17 0 0
## 72 HPV18, HPV16, HPV4, HPV17 0 0
## 73 HPV18, HPV16, HPV4, HPV17 0 0
## 74 HPV18, HPV16, HPV4, HPV17 0 0
## 75 HPV18, HPV16, HPV4, HPV17 0 0
## 76 HPV18, HPV16, HPV4, HPV17 0 0
## 77 HPV18, HPV16, HPV4, HPV17 0 0
## 78 HPV18, HPV16, HPV4, HPV17 0 0
## 79 HPV18, HPV16, HPV4, HPV17 0 0
## 80 HPV18, HPV16, HPV4, HPV17 0 0
## 81 HPV18, HPV16, HPV4, HPV17 0 0
## 82 HPV18, HPV16, HPV4, HPV17 0 0
## 83 HPV18, HPV16, HPV4, HPV17 0 0
## 84 HPV18, HPV16, HPV4, HPV17 0 0
## 85 HPV18, HPV16, HPV4, HPV17 0 0
## 86 HPV18, HPV16, HPV4, HPV17 0 0
## 87 HPV18, HPV16, HPV4, HPV17 0 0
## 88 HPV18, HPV16, HPV4, HPV17 0 0
## 89 HPV18, HPV16, HPV4, HPV17 0 0
## 90 HPV18, HPV16, HPV4, HPV17 0 0
## 91 HPV18, HPV16, HPV4, HPV17 0 0
## 92 HPV18, HPV16, HPV4, HPV17 0 0
## 93 HPV18, HPV16, HPV4, HPV17 0 0
## 94 HPV18, HPV16, HPV4, HPV17 0 0
## 95 HPV18, HPV16, HPV4, HPV17 0 0
## 96 HPV18, HPV16, HPV4, HPV17 0 0
## 97 HPV18, HPV16, HPV4, HPV17 0 0
## 98 HPV18, HPV16, HPV4, HPV17 0 0
## 99 HPV18, HPV16, HPV4, HPV17 0 0
## 100 HPV18, HPV16, HPV4, HPV17 0 0
##
## [[9]]
## forward_primer reverse_primer score coverage products
## 1 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGTT 0 0.2 0
## 2 GTTTGACCCCACTACACAGCG CACTAACACCAACGCCTAAAGGT 0 0.2 0
## 3 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 4 GTTTGACCCCACTACACAGCG ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 5 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCT 0 0.2 0
## 6 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 7 GTTTGACCCCACTACACAGCG ACTAACACCAACGCCTAAAGGTTG 0 0.2 0
## 8 GTTTGACCCCACTACACAGCG CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 9 GTTTGACCCCACTACACAGCG CCACTAACRCCAACRCCTAAAGG 0 0.2 0
## 10 GTTTGACCCCACTACACAGCG GGATGCCCACTAACACCAACG 0 0.2 0
## 11 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAAG 0 0.2 0
## 12 GTTTGACCCCACTACACAGCG GGCTGACCMCKGCCTACCTC 0 0.2 0
## 13 GTTTGACCCCACTACACAGCG GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 14 GTTTGACCCCACTACACAGCG TGCCCACTAACACCAACGC 0 0.2 0
## 15 GTTTGACCCCACTACACAGCG TGACCCCTGCCTACCTCC 0 0.2 0
## 16 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 17 GTTTGACCCCACTACACAGCG CAACGCCTAAAGGTTGACCCC 0 0.2 0
## 18 GTTTGACCCCACTACACAGCG CCAACGCCTAAAGGTTGACCC 0 0.2 0
## 19 GTTTGACCCCACTACACAGCG AGGTTGACCCCTGCCTACC 0 0.2 0
## 20 GTTTGACCCCACTACACAGCG ACCAACGCCTAAAGGTTGACC 0 0.2 0
## 21 GTTTGACCCCACTACACAGCG GCAATGGATGCCCACTAACACC 0 0.2 0
## 22 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 23 GTTTGACCCCACTACACAGCG ACACCAACGCCTAAAGGTTGAC 0 0.2 0
## 24 GTTTGACCCCACTACACAGCG AGCAATGGATGCCCACTAACAC 0 0.2 0
## 25 GTTTGACCCCACTACACAGCG TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 26 GTTTGACCCCACTACACAGCG ACCCCTGCCTACCTCCAAC 0 0.2 0
## 27 GTTTGACCCCACTACACAGCG ATGGATGCCCACTAACACCAAC 0 0.2 0
## 28 GTTTGACCCCACTACACAGCG CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 29 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTA 0 0.2 0
## 30 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 31 GTTTGACCCCACTACACAGCG CTAACACCAACGCCTAAAGGTTGA 0 0.2 0
## 32 GTTTGACCCCACTACACAGCG CACCYCTRCCTACCTCCA 0 0.2 0
## 33 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCA 0 0.2 0
## 34 GTTTGACCCCACTACACAGCG GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 35 GTTTGACCCCACTACACAGCG GCCCACTAACACCAACGCCTAA 0 0.2 0
## 36 GTTTGACCCCACTACACAGCG TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 37 GTTTGACCCCACTACACAGCG GACCCCTGCCTACCTCCAA 0 0.2 0
## 38 GTTTGACCCCACTACACAGCG CAATGGATGCCCACTAACACCAA 0 0.2 0
## 39 GTTTGACCCCACTACACAGCG CCCACTAACACCAACGCCTAAA 0 0.2 0
## 40 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCT 0 0.2 0
## 41 TGACCCCACTACACAGCGTT ACGCCTAAAGGTTGACCCCT 0 0.2 0
## 42 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCT 0 0.2 0
## 43 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACT 0 0.2 0
## 44 TGACCCCACTACACAGCGTT CGCCTAAAGGTTGACCCCTG 0 0.2 0
## 45 TGACCCCACTACACAGCGTT GGCTGACCMCKGCCTACCTC 0 0.2 0
## 46 TGACCCCACTACACAGCGTT GCCTAAAGGTTGACCCCTGC 0 0.2 0
## 47 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCC 0 0.2 0
## 48 TGACCCCACTACACAGCGTT AGGTTGACCCCTGCCTACC 0 0.2 0
## 49 TGACCCCACTACACAGCGTT GCAATGGATGCCCACTAACACC 0 0.2 0
## 50 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTAC 0 0.2 0
## 51 TGACCCCACTACACAGCGTT AGCAATGGATGCCCACTAACAC 0 0.2 0
## 52 TGACCCCACTACACAGCGTT TGTTTAGCAATGGATGCCCACTAAC 0 0.2 0
## 53 TGACCCCACTACACAGCGTT ATGGATGCCCACTAACACCAAC 0 0.2 0
## 54 TGACCCCACTACACAGCGTT CCTAAAGGTTGACCCCTGCCTA 0 0.2 0
## 55 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTA 0 0.2 0
## 56 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCA 0 0.2 0
## 57 TGACCCCACTACACAGCGTT GTTTAGCAATGGATGCCCACTAACA 0 0.2 0
## 58 TGACCCCACTACACAGCGTT TTGTTTAGCAATGGATGCCCACTAA 0 0.2 0
## 59 TGACCCCACTACACAGCGTT CAATGGATGCCCACTAACACCAA 0 0.2 0
## 60 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGT 0 0.2 0
## 61 TCCTTGCTGTGGGACATCCAT CACGCCCATACTAAACGCTGT 0 0.2 0
## 62 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGT 0 0.2 0
## 63 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGT 0 0.2 0
## 64 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAGT 0 0.2 0
## 65 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCT 0 0.2 0
## 66 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCT 0 0.2 0
## 67 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACT 0 0.2 0
## 68 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGAT 0 0.2 0
## 69 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGAAT 0 0.2 0
## 70 TCCTTGCTGTGGGACATCCAT ACGCCCATACTAAACGCTGTG 0 0.2 0
## 71 TCCTTGCTGTGGGACATCCAT TGCCTACCTCCAACCCTGTG 0 0.2 0
## 72 TCCTTGCTGTGGGACATCCAT GCCCATACTAAACGCTGTGTAGTG 0 0.2 0
## 73 TCCTTGCTGTGGGACATCCAT GCACGCCCATACTAAACGCTG 0 0.2 0
## 74 TCCTTGCTGTGGGACATCCAT CCTGCCTACCTCCAACCCTG 0 0.2 0
## 75 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGATG 0 0.2 0
## 76 TCCTTGCTGTGGGACATCCAT CATACTAAACGCTGTGTAGTGGGG 0 0.2 0
## 77 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGG 0 0.2 0
## 78 TCCTTGCTGTGGGACATCCAT CCTCCAACCCTGTGCACG 0 0.2 0
## 79 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTAG 0 0.2 0
## 80 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGAG 0 0.2 0
## 81 TCCTTGCTGTGGGACATCCAT GTGGGGTCAAACAGAGATGAATCAG 0 0.2 0
## 82 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAG 0 0.2 0
## 83 TCCTTGCTGTGGGACATCCAT CTAAACGCTGTGTAGTGGGGTC 0 0.2 0
## 84 TCCTTGCTGTGGGACATCCAT GCCTACCTCCAACCCTGTGC 0 0.2 0
## 85 TCCTTGCTGTGGGACATCCAT TCCAACCCTGTGCACGC 0 0.2 0
## 86 TCCTTGCTGTGGGACATCCAT CCAACCCTGTGCACGCC 0 0.2 0
## 87 TCCTTGCTGTGGGACATCCAT CCCTGCCTACCTCCAACCC 0 0.2 0
## 88 TCCTTGCTGTGGGACATCCAT CCCCTGCCTACCTCCAACC 0 0.2 0
## 89 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATAC 0 0.2 0
## 90 TCCTTGCTGTGGGACATCCAT CCTACCTCCAACCCTGTGCAC 0 0.2 0
## 91 TCCTTGCTGTGGGACATCCAT ACCCCTGCCTACCTCCAAC 0 0.2 0
## 92 TCCTTGCTGTGGGACATCCAT CCTGTGCACGCCCATACTAAAC 0 0.2 0
## 93 TCCTTGCTGTGGGACATCCAT CGCTGTGTAGTGGGGTCAAAC 0 0.2 0
## 94 TCCTTGCTGTGGGACATCCAT CGCCCATACTAAACGCTGTGTA 0 0.2 0
## 95 TCCTTGCTGTGGGACATCCAT GGGGTCAAACAGAGATGAATCAGGTA 0 0.2 0
## 96 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATACTA 0 0.2 0
## 97 TCCTTGCTGTGGGACATCCAT CCCTGTGCACGCCCATA 0 0.2 0
## 98 TCCTTGCTGTGGGACATCCAT TGTAGTGGGGTCAAACAGAGATGA 0 0.2 0
## 99 TCCTTGCTGTGGGACATCCAT TGTGTAGTGGGGTCAAACAGAGA 0 0.2 0
## 100 TCCTTGCTGTGGGACATCCAT GCTGTGTAGTGGGGTCAAACAGA 0 0.2 0
## similar_signatures missing_signatures enzyme digest_score fragments
## 1 HPV18, HPV16, HPV4, HPV17 0 0
## 2 HPV18, HPV16, HPV4, HPV17 0 0
## 3 HPV18, HPV16, HPV4, HPV17 0 0
## 4 HPV18, HPV16, HPV4, HPV17 0 0
## 5 HPV18, HPV16, HPV4, HPV17 0 0
## 6 HPV18, HPV16, HPV4, HPV17 0 0
## 7 HPV18, HPV16, HPV4, HPV17 0 0
## 8 HPV18, HPV16, HPV4, HPV17 0 0
## 9 HPV18, HPV16, HPV4, HPV17 0 0
## 10 HPV18, HPV16, HPV4, HPV17 0 0
## 11 HPV18, HPV16, HPV4, HPV17 0 0
## 12 HPV18, HPV16, HPV4, HPV17 0 0
## 13 HPV18, HPV16, HPV4, HPV17 0 0
## 14 HPV18, HPV16, HPV4, HPV17 0 0
## 15 HPV18, HPV16, HPV4, HPV17 0 0
## 16 HPV18, HPV16, HPV4, HPV17 0 0
## 17 HPV18, HPV16, HPV4, HPV17 0 0
## 18 HPV18, HPV16, HPV4, HPV17 0 0
## 19 HPV18, HPV16, HPV4, HPV17 0 0
## 20 HPV18, HPV16, HPV4, HPV17 0 0
## 21 HPV18, HPV16, HPV4, HPV17 0 0
## 22 HPV18, HPV16, HPV4, HPV17 0 0
## 23 HPV18, HPV16, HPV4, HPV17 0 0
## 24 HPV18, HPV16, HPV4, HPV17 0 0
## 25 HPV18, HPV16, HPV4, HPV17 0 0
## 26 HPV18, HPV16, HPV4, HPV17 0 0
## 27 HPV18, HPV16, HPV4, HPV17 0 0
## 28 HPV18, HPV16, HPV4, HPV17 0 0
## 29 HPV18, HPV16, HPV4, HPV17 0 0
## 30 HPV18, HPV16, HPV4, HPV17 0 0
## 31 HPV18, HPV16, HPV4, HPV17 0 0
## 32 HPV18, HPV16, HPV4, HPV17 0 0
## 33 HPV18, HPV16, HPV4, HPV17 0 0
## 34 HPV18, HPV16, HPV4, HPV17 0 0
## 35 HPV18, HPV16, HPV4, HPV17 0 0
## 36 HPV18, HPV16, HPV4, HPV17 0 0
## 37 HPV18, HPV16, HPV4, HPV17 0 0
## 38 HPV18, HPV16, HPV4, HPV17 0 0
## 39 HPV18, HPV16, HPV4, HPV17 0 0
## 40 HPV18, HPV16, HPV4, HPV17 0 0
## 41 HPV18, HPV16, HPV4, HPV17 0 0
## 42 HPV18, HPV16, HPV4, HPV17 0 0
## 43 HPV18, HPV16, HPV4, HPV17 0 0
## 44 HPV18, HPV16, HPV4, HPV17 0 0
## 45 HPV18, HPV16, HPV4, HPV17 0 0
## 46 HPV18, HPV16, HPV4, HPV17 0 0
## 47 HPV18, HPV16, HPV4, HPV17 0 0
## 48 HPV18, HPV16, HPV4, HPV17 0 0
## 49 HPV18, HPV16, HPV4, HPV17 0 0
## 50 HPV18, HPV16, HPV4, HPV17 0 0
## 51 HPV18, HPV16, HPV4, HPV17 0 0
## 52 HPV18, HPV16, HPV4, HPV17 0 0
## 53 HPV18, HPV16, HPV4, HPV17 0 0
## 54 HPV18, HPV16, HPV4, HPV17 0 0
## 55 HPV18, HPV16, HPV4, HPV17 0 0
## 56 HPV18, HPV16, HPV4, HPV17 0 0
## 57 HPV18, HPV16, HPV4, HPV17 0 0
## 58 HPV18, HPV16, HPV4, HPV17 0 0
## 59 HPV18, HPV16, HPV4, HPV17 0 0
## 60 HPV18, HPV16, HPV4, HPV17 0 0
## 61 HPV18, HPV16, HPV4, HPV17 0 0
## 62 HPV18, HPV16, HPV4, HPV17 0 0
## 63 HPV18, HPV16, HPV4, HPV17 0 0
## 64 HPV18, HPV16, HPV4, HPV17 0 0
## 65 HPV18, HPV16, HPV4, HPV17 0 0
## 66 HPV18, HPV16, HPV4, HPV17 0 0
## 67 HPV18, HPV16, HPV4, HPV17 0 0
## 68 HPV18, HPV16, HPV4, HPV17 0 0
## 69 HPV18, HPV16, HPV4, HPV17 0 0
## 70 HPV18, HPV16, HPV4, HPV17 0 0
## 71 HPV18, HPV16, HPV4, HPV17 0 0
## 72 HPV18, HPV16, HPV4, HPV17 0 0
## 73 HPV18, HPV16, HPV4, HPV17 0 0
## 74 HPV18, HPV16, HPV4, HPV17 0 0
## 75 HPV18, HPV16, HPV4, HPV17 0 0
## 76 HPV18, HPV16, HPV4, HPV17 0 0
## 77 HPV18, HPV16, HPV4, HPV17 0 0
## 78 HPV18, HPV16, HPV4, HPV17 0 0
## 79 HPV18, HPV16, HPV4, HPV17 0 0
## 80 HPV18, HPV16, HPV4, HPV17 0 0
## 81 HPV18, HPV16, HPV4, HPV17 0 0
## 82 HPV18, HPV16, HPV4, HPV17 0 0
## 83 HPV18, HPV16, HPV4, HPV17 0 0
## 84 HPV18, HPV16, HPV4, HPV17 0 0
## 85 HPV18, HPV16, HPV4, HPV17 0 0
## 86 HPV18, HPV16, HPV4, HPV17 0 0
## 87 HPV18, HPV16, HPV4, HPV17 0 0
## 88 HPV18, HPV16, HPV4, HPV17 0 0
## 89 HPV18, HPV16, HPV4, HPV17 0 0
## 90 HPV18, HPV16, HPV4, HPV17 0 0
## 91 HPV18, HPV16, HPV4, HPV17 0 0
## 92 HPV18, HPV16, HPV4, HPV17 0 0
## 93 HPV18, HPV16, HPV4, HPV17 0 0
## 94 HPV18, HPV16, HPV4, HPV17 0 0
## 95 HPV18, HPV16, HPV4, HPV17 0 0
## 96 HPV18, HPV16, HPV4, HPV17 0 0
## 97 HPV18, HPV16, HPV4, HPV17 0 0
## 98 HPV18, HPV16, HPV4, HPV17 0 0
## 99 HPV18, HPV16, HPV4, HPV17 0 0
## 100 HPV18, HPV16, HPV4, HPV17 0 0
# TYPE <- 'length'
# LEVELS <- 2
# MIN_SIZE <- 200
# MAX_SIZE <- 1400
# RESOLUTION <- c(
# seq(200, 700, 3),
# seq(705, 1000, 5),
# seq(1010, 1400, 10)
# )
#
# TYPE <- 'melt'
# MIN_SIZE <- 55
# MAX_SIZE <- 400FOCUS_ID <- 'HPV18'
params <- expand.grid(
enzymes = lapply(1:3, function(x)
RESTRICTION_ENZYMES[
sample(1:length(RESTRICTION_ENZYMES), 3)
]
),
minProductSize = seq(80, 150, length.out = 3),
maxProductSize = seq(500, 5000, length.out = 3),
resolution = seq(1, 2, length.out = 3),
levels = seq(5, 20, length.out = 3)
) %>% mutate(type = rep('melt', 243))
gridsearch <- apply(params, 1, function(...)
list(
arg = as.list(...),
out = do.call(
DesignSignatures,
append(
list(
dbFile = dbConn,
tblName = 'Seqs',
identifier = '',
focusID = FOCUS_ID
),
as.list(...)
)
)
)
) %>% bind_rows
objective <- function(x) {
print(x)
}https://www.ncbi.nlm.nih.gov/nuccore
"Human papillomavirus"[Primary Organism]
AND viruses[filter]
NOT Polyamides[All Fields]
NOT Method[All Fields]
NOT Patent[All Fields]
AND Anal[All Fields]